debian-science-1.0ubuntu1/0000755000000000000000000000000012264702434012421 5ustar debian-science-1.0ubuntu1/config/0000755000000000000000000000000012132747623013671 5ustar debian-science-1.0ubuntu1/config/config.10000644000000000000000000000111411415045022015200 0ustar .TH science-config 1 "Apr 03, 2008" "Debian Science" .SH NAME .B science-config \- Debian Science common metapackage helper .B science- \- package information and auto-apt helper .SH SYNOPSIS .B science-config .B science- .SH DESCRIPTION Print just a simple information page about every science-* package of the Debian Science Blend. Each metapackage contains a .I /usr/bin/science- file which should print some useful information and could be used as auto-apt helper. .SH AUTHORS Debian Science debian-science-1.0ubuntu1/config/config0000755000000000000000000000027211360134132015050 0ustar #!/bin/sh ## Prints some info about that package and lets auto-apt work dpkg --status `basename $0` | \ grep -v ^Priority | \ grep -v ^Section | \ grep -v ^Installed-Size debian-science-1.0ubuntu1/config/conf0000644000000000000000000000052611360134132014527 0ustar ## This is a configuration file for Debian Science Blend ## It is read after /etc/blends/blends.conf and can override or add variables ## This variable is replaced by a debconf question ## UPDATEUSERMENU=yes ## Some Blends do not build their name generic like "Debian #BLEND#" so ## we need the correct name here BLENDNAME="Debian Science" debian-science-1.0ubuntu1/config/control0000644000000000000000000000654712132747623015310 0ustar Package: science-config Architecture: all Depends: adduser, ${misc:Depends}, menu, blends-common (>= 0.6.15) Description: Debian Science Project config package This package provides the basic infrastructure of all science-* packages and is needed by them. . These are the science related metapackages in the Debian Science project: . * science-astronomy packages related to astronomy * science-astronomy-dev packages related to development of astronomical applications * science-biology packages related to biology * science-chemistry packages related to chemistry * science-dataacquisition packages related to data acquisition * science-dataacquisition-dev packages related to data acquisition development * science-distributedcomputing distributed computing packages * science-electrophysiology packages related to electrophysiology * science-electronics packages related to electronics * science-engineering packages related to engineering * science-engineering-dev packages related to development of engineering applications * science-geography packages related to geography * science-highenergy-physics packages related to high energy physics * science-highenergy-physics-dev packages related to development of high energy physics applications * science-linguistics packages related to linguistics * science-machine-learning packages related to machine learning * science-mathematics packages related to mathematics * science-mathematics-dev packages related to development of mathematical applications * science-meteorology packages related to meteorology and climate * science-meteorology-dev packages related to the development of meteorology and climate applications * science-nanoscale-physics packages related to nanoscale physics * science-nanoscale-physics-dev packages useful for developing nanoscale physics applications * science-neuroscience-cognitive packages related to cognitive neuroscience * science-neuroscience-datasets packages for Neuroscience Datasets * science-neuroscience-modeling packages for modeling of neural systems * science-physics packages related to physics * science-physics-dev packages related to physics development of physical applications * science-psychophysics packages related to packages for psychophysics * science-robotics packages related to robotics * science-simulation packages to do simulations . This are metapackages for common utilities for all sciences: . * science-imageanalysis packages related to image analysis * science-numericalcomputation packages related to numerical computation * science-statistics packages related to statistics * science-typesetting packages related to typesetting * science-viewing packages related to viewing . Note: All these packages are so called metapackages. This means they are not executable programs, but only links to other packages. This way you will conveniently get most of scientific free software which is available in Debian. debian-science-1.0ubuntu1/.bzr-builddeb/0000755000000000000000000000000012264700327015043 5ustar debian-science-1.0ubuntu1/.bzr-builddeb/default.conf0000644000000000000000000000003112264700327017330 0ustar [BUILDDEB] native = True debian-science-1.0ubuntu1/COPYING0000644000000000000000000010451311360134132013446 0ustar GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The GNU General Public License is a free, copyleft license for software and other kinds of works. The licenses for most software and other practical works are designed to take away your freedom to share and change the works. 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The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read . debian-science-1.0ubuntu1/debian/0000755000000000000000000000000012264702570013644 5ustar debian-science-1.0ubuntu1/debian/copyright0000644000000000000000000000226411360134132015570 0ustar X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat X-Debianized-By: Frederic Daniel Luc Lehobey , Andreas Tille X-Debinized-Date: Mon, 23 Jul 2007 09:18:16 +0200. Files: * Copyright: © 2007-2009 Frederic Daniel Luc Lehobey , Andreas Tille and others License: GPL-2+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. X-Comment: On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-2'. debian-science-1.0ubuntu1/debian/changelog0000644000000000000000000003276112264702543015527 0ustar debian-science (1.0ubuntu1) trusty; urgency=medium * Merge with Debian; remaining changes: - libcneartree3-dev (NBS) -> libcneartree-dev - nordugrid-arc-nox (NBS) -> libarccommon2 - python-mapnik (NBS) -> python-mapnik2 - Remove r-cran-pscl (NBS) - Regenerate debian/control and debian-science-tasks.desc - libteem1 (NBS) -> libteem2 - openturns-wrapper (NBS) -> openturns-examples - Remove proofgeneral-coq (NBS) - science-engineering-dev: Remove dependency on deal.ii-dev, removed in quantal (NBS). - science-dataacquisition-dev: Follow SOVER bump in libtango8-dev. - Move postgis to 9.3 (Closes: #732414) - Drop explicit libopenmpi1.3 dependencies, the current default openmpi implementation is pulled in my openmpi-bin. * tasks/mathematics: Drop fenics and dolfin-bin, NBS. * tasks/mathematics-dev: Drop dolfin-dev, NBS. -- Matthias Klose Mon, 13 Jan 2014 06:49:58 +0100 debian-science (1.0) unstable; urgency=low * Update metapackages for Wheezy * debian/control, debian-gis-tasks.desc: Usual changes of dependency based on the resolving of new packages in Debian as specified in the tasks files [ Sylvestre Ledru ] * tasks/robotics: add some more dependencies. [ Andreas Tille ] * debian/tasks/simulation: Add new task for simulations * debian/tasks/physics-dev: Add new task for development of physical applications [ Picca Frédéric-Emmanuel ] * tasks/dataacquisition: Add python-taurus * tasks/{mathematics, numericalcomputation, physics, simulation}: Add python-deap * tasks/{chemistry, nanoscale-physics, physics, simulations}: Add fdmnes [ Andreas Tille ] * tasks/highenergy-physics-dev: Create metapackage targeting at development of high energy physics applications -- Andreas Tille Mon, 15 Apr 2013 10:39:06 +0200 debian-science (0.16ubuntu5) trusty; urgency=medium * Drop explicit libopenmpi1.3 dependencies, the current default openmpi implementation is pulled in my openmpi-bin. -- Dimitri John Ledkov Tue, 24 Dec 2013 11:28:41 +0000 debian-science (0.16ubuntu4) trusty; urgency=medium * Move postgis to 9.3 (Closes: #732414) -- Martin Pitt Wed, 18 Dec 2013 08:43:56 +0100 debian-science (0.16ubuntu3) saucy; urgency=low * science-dataacquisition-dev: Follow SOVER bump in libtango8-dev. -- Adam Conrad Wed, 29 May 2013 23:50:06 -0600 debian-science (0.16ubuntu2) quantal; urgency=low * science-engineering-dev: Remove dependency on deal.ii-dev, removed in quantal (NBS). -- Matthias Klose Tue, 11 Sep 2012 16:06:49 +0200 debian-science (0.16ubuntu1) quantal; urgency=low * Merge from Debian testing. Remaining changes: - libcneartree3-dev (NBS) -> libcneartree-dev - nordugrid-arc-nox (NBS) -> libarccommon2 - python-mapnik (NBS) -> python-mapnik2 - Remove r-cran-pscl (NBS) - Regenerate debian/control and debian-science-tasks.desc * libteem1 (NBS) -> libteem2 * openturns-wrapper (NBS) -> openturns-examples * Remove proofgeneral-coq (NBS) -- Michael Terry Mon, 02 Jul 2012 23:11:58 -0400 debian-science (0.16) unstable; urgency=low [ Joost van Baal-Ilić ] * tasks/linguistics: add some more dependencies. [ Andreas Tille ] * debian/control(.stub) Standards-Version: 3.9.3 (no changes needed) * debian/control: Usual changes of dependency based on the resolving of new packages in Debian as specified in the tasks files * tasks/{robotics,numericalcomputation,mathematics}: s/octave3.2/octave/ Closes: #667587 -- Andreas Tille Fri, 30 Dec 2011 08:45:03 +0100 debian-science (0.15ubuntu1) precise; urgency=low * Merge from Debian testing. Remaining changes: - tasks/geography: Move to postgresql-9.1-postgis (8.4 is NBS), switch to python-mapnik2 from python-mapnik (NBS). - tasks/statistics: Remove r-cran-pscl (NBS). - Switch to libcneartree-dev from libcneartree3-dev (NBS). - Switch from nordugrid-arc-nox to libarccommon1. - Regenerated debian/control; This also cleaned up some more dependencies to packages which do not exist any more. -- James Page Tue, 24 Jan 2012 08:16:50 +0000 debian-science (0.15) unstable; urgency=low * config/control: Mention new metapackage science-highenergy-physics (which was lacking in last changelog) * tasks/dataacquisition-dev: New metapackage to develop data aquisition applications * tasks/statistics: s/r-cran-design/r-cran-rms/ Closes: #649446 * tasks/distributedcomputing: - s/mpichpython/openmpipython/ - s/lampython/mpich2python/ Closes: #646417 -- Andreas Tille Sat, 17 Dec 2011 23:56:58 +0100 debian-science (0.14ubuntu1) precise; urgency=low * Merge from Debian testing. Remaining changes: - tasks/geography: Move to postgresql-9.1-postgis (8.4 is NBS), switch to python-mapnik2 from python-mapnik (NBS). - tasks/statistics: Remove r-cran-pscl (NBS). - Switch to libcneartree-dev from libcneartree3-dev (NBS). - Switch from nordugrid-arc-nox to libarccommon1. - Regenerated debian/control; This also cleaned up some more dependencies to packages which do not exist any more. -- James Page Mon, 05 Dec 2011 11:09:15 +0000 debian-science (0.14) unstable; urgency=low * tasks/engineering-dev: Deleted libqwt5-qt3-dev which will be removed from Debian Closes: #629869 * tasks/astronomy(-dev): Added several packages according to a hint of Luk Claes Closes: #633562 * tasks/physics: s/quantumespresso/quantum-espresso/ Closes: #646701 * Fixed Vcs fields * Removed explicite Build-Dependency because it is implicitely given by Build-Depending blends-dev -- Andreas Tille Fri, 28 Oct 2011 12:36:56 +0200 debian-science (0.13ubuntu3) oneiric; urgency=low * debian-science-tasks.desc, tasks/geography: Move to postgresql-9.1-postgis (8.4 is NBS). * debian-science-tasks.desc, tasks/statistics: Remove r-cran-pscl (NBS). * Regenerate debian/control. This also cleaned up some more dependencies to packages which do not exist any more. -- Martin Pitt Tue, 27 Sep 2011 13:33:30 +0200 debian-science (0.13ubuntu2) oneiric; urgency=low * Switch to libcneartree-dev from libcneartree3-dev which was NBS -- Jeremy Bicha Wed, 24 Aug 2011 11:29:09 +0100 debian-science (0.13ubuntu1) oneiric; urgency=low * Switch from nordugrid-arc-nox to libarccommon1. -- Colin Watson Wed, 17 Aug 2011 15:55:55 +0100 debian-science (0.13) unstable; urgency=low [ Sylvestre Ledru ] * libmatheval1-dev => libmatheval-dev (Closes: #612758) [ Andreas Tille ] * Standards-Version: 3.9.2 (no changes needed) * New metapackages: - science-bci brain-computer interface - science-distributedcomputing distributed computing packages - science-electrophysiology packages related to electrophysiology - science-nanoscale-physics packages related to nanoscale physics - science-nanoscale-physics-dev packages useful for developing nanoscale physics applications - science-neuroscience-datasets packages for Neuroscience Datasets - science-neuroscience-modeling packages for modeling of neural systems - science-psychophysics packages related to packages for psychophysics * Several new dependencies auto generated via Blends tools -- Andreas Tille Wed, 04 May 2011 11:34:38 +0200 debian-science (0.12) unstable; urgency=low * tasks/statistics: Fix typo in package description Closes: #592701 * config/control: Depends: blends-common (>= 0.6.15) * debian/control.stub: Build-Depends-Indep: blends-dev (>= 0.6.15) Closes: #601959 * New tasks: science-nanoscale-physics and science-nanoscale-physics-dev -- Andreas Tille Mon, 08 Nov 2010 16:14:37 +0100 debian-science (0.11) unstable; urgency=low [ Sylvestre Ledru ] * hkl package added * salome is now in debian. Removing description [ Andreas Tille ] * New task: machine-learning * tasks/robotics: libvtk5 -> libvtk5.4 Closes: #591444 * Several prospective packages are now official Debian packages and this included automatically via blends-dev build mechanism * Standards-Version: 3.9.1 (no changes needed) * Build-Depends: blends-dev (>= 0.6.14) -- Andreas Tille Tue, 03 Aug 2010 09:46:09 +0200 debian-science (0.10) unstable; urgency=low * Rebuild against blends-dev >= 0.6.12. This results in using a prerm script instead of postrm which ensures that blends-common is installed while this script is running * Standards-Version: 3.8.4 (no changes needed) -- Andreas Tille Thu, 18 Mar 2010 09:26:14 +0100 debian-science (0.9) unstable; urgency=low * Depend from blends-common >= 0.6.9 and explain in NEWS.Debian that no attempt to take over any CDD related configuration Closes: #562554 -- Andreas Tille Sun, 24 Jan 2010 13:39:58 +0100 debian-science (0.8) unstable; urgency=low [ Sylvestre Ledru ] * Many packages updates * Some cleanup * Change of my email address [ Andreas Tille ] * config/control: Depends: blends-common (>= 0.6.8), which really Closes: #542658 * tasks/geography: s/postgresql-8.3-postgis/postgresql-8.4-postgis/ Closes: #559601 -- Andreas Tille Wed, 09 Dec 2009 20:12:09 +0100 debian-science (0.7) unstable; urgency=low [ Andreas Tille ] * Change section of metapackages from misc to science * debian/control.stub: - Fixed Vcs-Svn (missing svn/) - Build-Depends: blends-dev (>= 0.6.6) * config/control: Depends: blends-common (>= 0.6.6) Closes: #542658 * Debhelper 7 * Standards-Version: 3.8.3 (no changes needed) [ Alastair McKinstry ] * Added files to tasks/meteorology and tasks/meteorology-dev. -- Andreas Tille Fri, 21 Aug 2009 14:20:43 +0200 debian-science (0.6) unstable; urgency=low [ Andreas Tille ] * tasks/electronics: - removed vipec which is not in Debian any more - Increased dependency from Suggests to Depends for electric because it is not orphaned any more * tasks/physics: - lowercase prospective packages ESPResSo++ and PWscf Closes: #523077 * debian/control.stub: increased version of blends-dev dependency to 0.6.3 to make sure all package names will be lower cased [ Alastair McKinstry ] * Added science-meteorology and science-meteorology-dev metapackages. * tasks/meteorology: - Added. Depend on cdo and DB-All.e * tasks/meteorology-dev: - Added. Depend on libemos-dev. -- Andreas Tille Tue, 14 Apr 2009 10:51:31 +0200 debian-science (0.5) unstable; urgency=low [ Andreas Tille ] * tasks/mathematics-dev: replace libs by lib-devels Closes: #515947 * Vcs fields were fixed in previous version but closing the bug here which was reported later while the package was sitting in new Closes: #515943 * science-mathematics: s/Depends: Isabelle/Depends: isabelle/ Closes: #518048 * Bumped policy to 3.8.1 and make use of the new feature that debian/control allows comment lines starting with # with no preceding whitespace. [Policy paragraph 5.2] * tasks/geography: Depend from proj-bin instead of proj Closes: #521819 * Machine readable copyright file * Enhanced long desriptions for those tasks where lintian claimed about extended-description-is-probably-too-short [ Michael Hanke ] * Added preliminary task for cognitive neuroscience. -- Andreas Tille Thu, 02 Apr 2009 11:50:18 +0200 debian-science (0.4) experimental; urgency=low * Use blends-dev instead of cdd-dev * Adapted Vcs fields to new location (cdd -> blends) * New metapackages: astronomy-dev, dataacquisition, engineering-dev, imageanalysis, numericalcomputation -- Andreas Tille Tue, 06 Jan 2009 09:34:13 +0100 debian-science (0.3) unstable; urgency=low * Some applications / libraries added (Closes: #491474) * Add myself as uploader -- Sylvestre Ledru Sat, 19 Jul 2008 20:06:41 +0200 debian-science (0.2) unstable; urgency=low * tasks/geography: removed hyphen from description Closes: #486929 * tasks/astronomy: Added descriptions for packages that vanished from Debian * tasks/*: s/Depends/Recommens/ - this is done by current cdd-dev anyway The rationale for this behaviour is explained there. It seems logical to state in the tasks files what finally is implemented. We might think about enabling real Depends later if there might be reasons for this. * Current cdd-gen-control does not handle Recommends properly and thus all Recommends in tasks files were turned to Depends. * tasks/engineering: New task with some new dependencies and some moved from tasks/physics to this place Closes: #488962 -- Andreas Tille Thu, 03 Jul 2008 08:28:52 +0200 debian-science (0.1) unstable; urgency=low [ Frederic Daniel Luc Lehobey ] * Initial Release. [ Andreas Tille ] * DM-Upload-Allowed: yes * Vcs-Browser, Vcs-Svn * debian-science-maintainers@lists.alioth.debian.org as maintainer * cdd-dev >= 0.5.2 * Standards-Version: 3.8.0 -- Andreas Tille Sat, 07 Jun 2008 00:30:31 +0200 debian-science-1.0ubuntu1/debian/NEWS.Debian0000644000000000000000000000074611360134132015520 0ustar debian-science (0.9) unstable; urgency=low In former Debian releases todays Debian Pure Blends were called Custom Debian Distributions. The related tools might have dropped some configuration files in /etc/cdd. The only use were to control user menus stuff which was rarely used. If you never changed any file in /etc/cdd/med you can ignore this. If not please take over the changes to /etc/blends/med. -- Andreas Tille Sun, 24 Jan 2010 13:39:58 +0100 debian-science-1.0ubuntu1/debian/control.stub0000644000000000000000000000162111737244657016236 0ustar Source: debian-science Section: science Priority: extra Maintainer: Debian Science Team DM-Upload-Allowed: yes Uploaders: Frederic Daniel Luc Lehobey , Andreas Tille , Sylvestre Ledru Build-Depends-Indep: blends-dev (>= 0.6.15) Standards-Version: 3.9.3 Homepage: http://wiki.debian.org/DebianScience/ Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/science/trunk/debian-science/ Vcs-Svn: svn://svn.debian.org/blends/projects/science/trunk/debian-science/ Package: science-tasks Architecture: all Depends: tasksel Description: Debian Science tasks for tasksel This package is part of the Debian Pure Blend "Debian Science" and provides additional tasks for tasksel. If this package will be installed all tasks which are provided by Debian Science will be added to the tasksel menu. debian-science-1.0ubuntu1/debian/compat0000644000000000000000000000000211360134132015027 0ustar 7 debian-science-1.0ubuntu1/debian/control0000644000000000000000000011620712264701230015246 0ustar # This file is autogenerated via make -f debian/rules dist. Do not edit! Source: debian-science Section: science Priority: extra Maintainer: Debian Science Team DM-Upload-Allowed: yes Uploaders: Frederic Daniel Luc Lehobey , Andreas Tille , Sylvestre Ledru Build-Depends-Indep: blends-dev (>= 0.6.15) Standards-Version: 3.9.3 Homepage: http://wiki.debian.org/DebianScience/ Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/science/trunk/debian-science/ Vcs-Svn: svn://svn.debian.org/blends/projects/science/trunk/debian-science/ Package: science-tasks Architecture: all Depends: tasksel Description: Debian Science tasks for tasksel This package is part of the Debian Pure Blend "Debian Science" and provides additional tasks for tasksel. If this package will be installed all tasks which are provided by Debian Science will be added to the tasksel menu. Package: science-config Architecture: all Depends: adduser, ${misc:Depends}, menu, blends-common (>= 0.6.15) Description: Debian Science Project config package This package provides the basic infrastructure of all science-* packages and is needed by them. . These are the science related metapackages in the Debian Science project: . * science-astronomy packages related to astronomy * science-astronomy-dev packages related to development of astronomical applications * science-biology packages related to biology * science-chemistry packages related to chemistry * science-dataacquisition packages related to data acquisition * science-dataacquisition-dev packages related to data acquisition development * science-distributedcomputing distributed computing packages * science-electrophysiology packages related to electrophysiology * science-electronics packages related to electronics * science-engineering packages related to engineering * science-engineering-dev packages related to development of engineering applications * science-geography packages related to geography * science-highenergy-physics packages related to high energy physics * science-highenergy-physics-dev packages related to development of high energy physics applications * science-linguistics packages related to linguistics * science-machine-learning packages related to machine learning * science-mathematics packages related to mathematics * science-mathematics-dev packages related to development of mathematical applications * science-meteorology packages related to meteorology and climate * science-meteorology-dev packages related to the development of meteorology and climate applications * science-nanoscale-physics packages related to nanoscale physics * science-nanoscale-physics-dev packages useful for developing nanoscale physics applications * science-neuroscience-cognitive packages related to cognitive neuroscience * science-neuroscience-datasets packages for Neuroscience Datasets * science-neuroscience-modeling packages for modeling of neural systems * science-physics packages related to physics * science-physics-dev packages related to physics development of physical applications * science-psychophysics packages related to packages for psychophysics * science-robotics packages related to robotics * science-simulation packages to do simulations . This are metapackages for common utilities for all sciences: . * science-imageanalysis packages related to image analysis * science-numericalcomputation packages related to numerical computation * science-statistics packages related to statistics * science-typesetting packages related to typesetting * science-viewing packages related to viewing . Note: All these packages are so called metapackages. This means they are not executable programs, but only links to other packages. This way you will conveniently get most of scientific free software which is available in Debian. Package: science-astronomy Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: astronomical-almanac, boinc-app-milkyway, boinc-app-seti, esorex, ftools-fv, funtools, gcx, gpredict, gyoto, lightspeed, lynkeos.app, openuniverse, predict, qfits-tools, saods9, savi, sextractor, stardata-common, stellarium, wcslib-tools, wcstools, xplanet, yorick-full Suggests: casacore-tools, gliese, heasoft-fv, linoccult, midas, orbfit, pdl, pgplot5, python-scientific, scilab-celestlab, scilab-overload, scilab-scimysql, seesat5, spacechart, ssystem, stars, sunclock, worldwind, xephem, xorsa, xtide, xtide-data, yale, yorick-cubeview, yorick-mira, yorick-spydr, yorick-yao Description: Debian Science Astronomy packages This metapackage will install Debian Science packages related to Astronomy. You might also be interested in field::astronomy debtag and, depending on your focus, in the education-astronomy metapackage. Package: science-astronomy-dev Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: libastro-fits-cfitsio-perl, libccfits-dev, libcfitsio3-dev, libcpl-dev, libnova-dev, libqfits-dev, libsofa-c-dev, libstarlink-ast-dev, libstarlink-pal-dev, libwcstools-dev, python-cpl, python-pyfits, python-pywcs, slang-cfitsio, wcslib-dev Suggests: casacore-dev, libgyoto0-dev, libworldwind-java, python-astropy-legacy Description: Debian Science Astronomy-dev packages This metapackage will install Debian Science packages which might be helpful for development of applications for Astronomy. . You might also be interested in the science-astronomy metapackage. Package: science-biology Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: bauble, critterding, med-bio Suggests: avida-base, genesis, med-bio-dev Description: Debian Science Biology packages This metapackage will install Debian Science packages related to Biology. You might also be interested in the field::biology debtag. . This metapackage makes use of the packages med-bio and med-bio-dev (for development of biological applications) which are maintained by Debian Med - another Debian Pure Blend. If you are a biologist you are most probably interested in the Debian Med project which deals with biology and medicine in much more detail then the more general Debian Science. Package: science-chemistry Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: adun.app, apbs, avogadro, bkchem, bodr, chemeq, chemical-mime-data, chemical-structures, chemtool, cp2k, drawxtl, easychem, freefoam, gabedit, galculator, gamgi, garlic, gausssum, gchempaint, gcrystal, gcu-bin, gcu-plugin, gdis, gdpc, gelemental, ghemical, gperiodic, gromacs | gromacs-mpich | gromacs-openmpi, jmol, kalzium, katomic, libcdk-java, massxpert, mmass, mmass-modules, mopac7-bin, mpqc, mpqc-support, openbabel, pdb2pqr, psi3, pyfai, pymol, python-mzml, python-openbabel, qutemol, rasmol, tandem-mass, v-sim, viewmol, xbs, xdrawchem, xmakemol-gl | xmakemol Suggests: fdmnes, gdpc-examples, gromacs-lam, libegad, libint, molden, molekel, openchrom, python-mzml-doc, tinker Description: Debian Science Chemistry packages This metapackage will install Debian Science packages related to Chemistry. You might also be interested in the field::chemistry debtag and, depending on your focus, in the education-chemistry metapackage. Package: science-dataacquisition Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: engauge-digitizer, g3data, ghkl, jaaa, libfreenect-dev, netcdf-bin Suggests: comedi-source, epics, gnudatalanguage, gpsd, hart, ktimetrace, libgpib-bin, linux-image-2.6-rt, mx-dataacquisition, narval-utils, opendap, plot-digitizer, python-pytango, python-sardana, python-taurus, python-visa, qtdmm, rt-tests, rtai, tango-accesscontrol, tango-db, tango-starter, xenomai-runtime Description: Debian Science data acquisition packages This metapackage will install Debian Science packages related to data acquisition. This might be used in several sciences (as for instance science-viewing and science-typesetting). Package: science-distributedcomputing Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: condor, dmtcp, environment-modules, globus-core, gridengine-client, gridengine-exec, gridengine-master, gridengine-qmon, ipython, libarccommon2, mpich2, mpich2python, openmpi-bin, openmpipython, python-mpi, torque-common, torque-server Suggests: coop-computing-tools, hpcc, psom, python-mpi4py Description: Debian Science Distributed Computing packages This metapackage will install Debian Science packages useful for various types of distributed computing, such as grid-, cloud-, cluster- and parallel-computing. Package: science-electronics Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: arduino, arduino-core, avrdude, confluence, covered, electric, freehdl, fritzing, gcc-avr, geda, gerbv, gnucap, gplcver, gputils, gspiceui, iverilog, kicad, linsmith, oregano, pcb, qelectrotech, simulpic, texlive-latex-extra, tkgate, uisp, verilator, visolate, xsmc-calc Suggests: easyspice, geda-doc, geda-examples, ghdl, herb, kicad-doc-de, kicad-doc-en, kicad-doc-es, kicad-doc-fr, kicad-doc-it, kicad-doc-pt, kicad-doc-ru, klogic, ksimus, liblife-dev, ngspice, qucs, vbpp, vbs Description: Debian Science Electronics packages This metapackage will install Debian Science packages related to Electronics. You might also be interested in the field::electronics debtag and, depending on your focus, in the education-electronics metapackage. Package: science-electrophysiology Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: libdrawtk-dev, libgdf-dev, sigviewer Suggests: aghermann, bluespike, chronus, eeglab, eegview, klustakwik, libbiosig0, libeegdev-dev, libmcpanel-dev, librtfilter-dev, libxdffileio-dev, mclust, meabench, neo, neurodata, nspike, openelectrophy, patchclamp, pymeg, python-neuroshare, python-spykeutils, qrtailab, relacs, rtxi, science-dataacquisition, science-neuroscience-modeling, spike, spykeview, stimfit, trellis-neuro Description: Debian Science packages for Electrophysiology This metapackage will install Debian packages which might be useful for scientists doing electrophysiology-based neuroscience research. . The selection of packages is targeting the application of analysis techniques. Methods developers are referred to the science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging, and med-imaging-dev metapackages for a variety of additional software that might be useful for electrophysiology research. Package: science-engineering Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: cba, cgns-convert, code-aster-gui, code-saturne, freecad, freefoam, gerris, getdp, gmsh, hdfview, librecad, libsilo-bin, netgen, python-fiat, python-openturns, python-silo, pythoncad, sailcut, syrthes, z88 Suggests: avl, brlcad, ecs, life-apps, opencascade-draw, pycgns, r-cran-spc, salome, syfi-bin, tochnog, varkon Description: Debian Science Engineering packages This metapackage is part od the Debian Pure Blend "Debian Science" and installs packages related to Engineering. . Please not that there is an additional package engineering-dev which depends from packages which are useful to develop engineering related software. Package: science-engineering-dev Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: libadios-dev, libalberta2-dev, libbox-dev, libcgns-dev, libelmer-dev, libexodusii-dev, libgetfem++-dev, libhdf5-serial-dev, libitpp-dev, libjhdf4-java, libjhdf5-java, libmadlib-dev, libmed-dev, libmedc-dev, libmedimport-dev, libnetcdf-dev, libopenturns-dev, libsilo-dev, libxdmf-dev, python-netcdf, syfi-dev Suggests: freefoam-dev, libfvm-dev, libgtkdatabox-0.9.1-1-dev, libgtkdataboxmm-dev, liblife-dev, libluminate-dev, libmesh-dev, libnetcdf-java, libopencascade-dev, libqwt-dev | libqwt5-qt4-dev, libslepc3.0.0-dev, pycgns Description: Debian Science Engineering-dev packages This metapackage will install Debian Science packages which might be helpful for development of applications for Engineering. . You might also be interested in the science-engineering metapackage. Package: science-geography Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: avce00, drawmap, e00compr, gdal-bin, geoip-bin, gis-workstation, gmt, gosmore, gpsbabel, gpsd, gpsd-clients, gpsdrive, gpsman, gpsmanshp, gpstrans, gpx2shp, grass, grass-doc, imposm, josm, josm-plugins, mapnik-utils, mapserver-bin, merkaartor, ogdi-bin, openscenegraph, osm2pgsql, osmpbf-bin, pgadmin3, php5-mapscript, phppgadmin, postgis, proj-bin, python-mapnik2, qgis, qgis-plugin-grass, r-cran-mapdata, r-cran-mapproj, r-cran-maps, r-cran-sp, thuban, viking Suggests: earth3d, googleearth-package, grace6, openjump, postgresql-9.3-postgis, r-cran-maptools, sumo Description: Debian Science Geography packages This metapackage will install Debian Science packages related to Geography. You might also be interested in the field::geography debtag and, depending on your focus, in the education-geography metapackage. Package: science-highenergy-physics Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: cernlib, cernlib-base, cernlib-core, cernlib-extras, cernlib-montecarlo, dzedit, feynmf, geant321, herwig++, kuipc, kxterm, libroot-bindings-python5.34, libroot-bindings-ruby5.34, libroot-core5.34, libroot-geom5.34, libroot-graf2d-gpad5.34, libroot-graf2d-graf5.34, libroot-graf2d-postscript5.34, libroot-graf3d-eve5.34, libroot-graf3d-g3d5.34, libroot-graf3d-gl5.34, libroot-gui-ged5.34, libroot-gui5.34, libroot-hist-spectrum5.34, libroot-hist5.34, libroot-html5.34, libroot-io-xmlparser5.34, libroot-io5.34, libroot-math-foam5.34, libroot-math-genvector5.34, libroot-math-mathcore5.34, libroot-math-mathmore5.34, libroot-math-matrix5.34, libroot-math-minuit5.34, libroot-math-mlp5.34, libroot-math-physics5.34, libroot-math-quadp5.34, libroot-math-smatrix5.34, libroot-math-splot5.34, libroot-math-unuran5.34, libroot-misc-memstat5.34, libroot-misc-minicern5.34, libroot-misc-table5.34, libroot-montecarlo-eg5.34, libroot-montecarlo-vmc5.34, libroot-net-auth5.34, libroot-net-bonjour5.34, libroot-net-ldap5.34, libroot-net5.34, libroot-proof-proofplayer5.34, libroot-proof5.34, libroot-roofit5.34, libroot-tmva5.34, libroot-tree-treeplayer5.34, libroot-tree5.34, looptools, nypatchy, octave-lhapdf, paw, paw++, pawserv, pythia8-root-interface, python-lhapdf, python-rivet, rivet, rivet-plugins, rivet-root-converter, root-macro-fastjet, root-plugin-geom-gdml, root-plugin-geom-geombuilder, root-plugin-geom-geompainter, root-plugin-graf2d-asimage, root-plugin-graf2d-qt, root-plugin-graf2d-x11, root-plugin-graf3d-x3d, root-plugin-gui-fitpanel, root-plugin-gui-guibuilder, root-plugin-gui-qt, root-plugin-gui-sessionviewer, root-plugin-hist-hbook, root-plugin-hist-histpainter, root-plugin-hist-spectrumpainter, root-plugin-io-sql, root-plugin-io-xml, root-plugin-math-fftw3, root-plugin-math-fumili, root-plugin-math-minuit2, root-plugin-montecarlo-pythia8, root-plugin-net-globus, root-plugin-net-krb5, root-plugin-sql-mysql, root-plugin-sql-odbc, root-plugin-sql-pgsql, root-plugin-tree-treeviewer, root-system, root-system-bin, root-system-common, root-system-proofd, root-system-rootd, thepeg, thepeg-gui, zftp Suggests: geant321-doc, geant4, lhapdf-pdfsets-minimal, libroot-proof-clarens5.34, paw-demos, root-plugin-proof-peac, root-system-doc Description: Debian Science High Energy Physics packages This metapackage will install Debian Science packages related to High Energy Physics, which is a branch of physics that studies the elementary subatomic constituents of matter and radiation, and their interactions. The field is also called Particle Physics. . You might also be interested in the debtag field::physics and, depending on your focus, in the physics and education-physics metapackages. Package: science-highenergy-physics-dev Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: cernlib-base-dev, cernlib-core-dev, fcc, herwig++-dev, libclhep-dev, libfastjet-dev, libfastjet-fortran-dev, libfastjetplugins-dev, libfastjettools-dev, libhepmc-dev, libhepmcfio-dev, liblhapdf-dev, libooptools-dev, libpythia8-dev, librivet-dev, libroot-bindings-python-dev, libroot-bindings-ruby-dev, libroot-core-dev, libroot-geom-dev, libroot-graf2d-gpad-dev, libroot-graf2d-graf-dev, libroot-graf2d-postscript-dev, libroot-graf3d-eve-dev, libroot-graf3d-g3d-dev, libroot-graf3d-gl-dev, libroot-gui-dev, libroot-gui-ged-dev, libroot-hist-dev, libroot-hist-spectrum-dev, libroot-html-dev, libroot-io-dev, libroot-io-xmlparser-dev, libroot-math-foam-dev, libroot-math-genvector-dev, libroot-math-mathcore-dev, libroot-math-mathmore-dev, libroot-math-matrix-dev, libroot-math-minuit-dev, libroot-math-mlp-dev, libroot-math-physics-dev, libroot-math-quadp-dev, libroot-math-smatrix-dev, libroot-math-splot-dev, libroot-math-unuran-dev, libroot-misc-memstat-dev, libroot-misc-minicern-dev, libroot-misc-table-dev, libroot-montecarlo-eg-dev, libroot-montecarlo-vmc-dev, libroot-net-auth-dev, libroot-net-bonjour-dev, libroot-net-dev, libroot-net-ldap-dev, libroot-proof-dev, libroot-proof-proofplayer-dev, libroot-roofit-dev, libroot-static, libroot-tmva-dev, libroot-tree-dev, libroot-tree-treeplayer-dev, libsiscone-dev, libsiscone-spherical-dev, libthepeg-dev, rivet-plugins-dev Suggests: clhep-doc, fastjet-doc, fastjet-examples, hepmc-examples, hepmc-reference-manual, hepmc-user-manual, lhapdf-ccwrap-doc, libhepmcinterface-dev, libroot-proof-clarens-dev, pythia8-doc-html, pythia8-doc-worksheet, pythia8-examples, rivet-plugins-doc, rivet-reference, rivet-user-manual, siscone-doc-html, siscone-doc-pdf, siscone-examples, thepeg-reference Description: Debian Science High Energy Physics development packages This metapackage will install Debian Science packages related to development of High Energy Physics applications, which is a branch of physics that studies the elementary subatomic constituents of matter and radiation, and their interactions. The field is also called Particle Physics. . You might also be interested in the debtag field::physics and, depending on your focus, in the physics and education-physics metapackages. Package: science-imageanalysis Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: gpiv, gpivtools, gwyddion, libcv-dev, libteem2 Suggests: cimg-dev, libsimage-dev, libvisad-java, scilab-sivp Description: Debian Science image analysis packages This metapackage will install Debian Science packages related to scientific image acquisition. This might be used in several sciences (as for instance science-dataacquisition, science-viewing and science-typesetting). Package: science-linguistics Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: apertium, artha, dimbl, frog, link-grammar, mbt, mbtserver, timbl, timblserver, ucto, wordnet Suggests: libfolia1-dev, libmbt0-dev, libtimbl3-dev, libtimblserver2-dev, libucto1-dev, python-timbl, wnsqlbuilder Description: Debian Science Linguistics packages This metapackage is part of the Debian Pure Blend "Debian Science" and installs packages related to Linguistics. Package: science-machine-learning Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: autoclass, gprolog, libcv-dev, libevocosm-dev, libfann-dev, libga-dev, liblinear-dev, libocas-dev, libroot-math-mlp-dev, libroot-montecarlo-vmc-dev, libroot-tmva-dev, libshogun-dev, libsvm-dev, libtorch3-dev, libvigraimpex-dev, lush, mcl, octave-ga, pgapack, python-genetic, python-mdp, python-mlpy, python-mvpa, python-opencv, python-pebl, python-pyevolve, python-pyke, python-pymc, python-scikits-learn, python-statsmodels, python-vigra, r-cran-amore, r-cran-bayesm, r-cran-class, r-cran-cluster, r-cran-mass, r-cran-mcmcpack, r-cran-mnp, r-cran-msm, root-system, scilab-ann, vowpal-wabbit, weka, yap Suggests: flann, libacovea-dev, libcomplearn-dev, libqsearch-dev, libshark-dev, lua-torch5, pybrain, python-orange, science-numericalcomputation, science-statistics, science-typesetting Description: Debian Science Machine Learning packages This metapackage will install Debian packages which might be useful for scientists interested in machine learning. Included packages range from knowledge-based (expert) inference systems to software implementing dominant nowadays statistical methods. Package: science-mathematics Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: agda, axiom, bliss, coq, freefem, freefem++, freefem3d, freemat, gap, geogebra, geomview, gerris, getdp, ginac-tools, gmsh, hol-light, libmatheval1, lp-solve, lrslib, mathomatic, matita, mcl, minisat, mumps-test, netgen, octave, pari-extra, pari-gp, polybori, polybori-gui, polylib-utils, proofgeneral, prover9, python-deap, python-ffc, python-openturns, qtoctave, regina-normal, rheolef, science-statistics, scilab, scilab-ann, scilab-scimax, scilab-sivp, scilab-swt, scotch, snappea, wxmaxima, xmaxima, xmds Suggests: eprover, isabelle, kseg, libgivaro0, life-apps, magnus, nauty, netgen-doc, octaviz, r-cran-evd, sagemath, singular Description: Debian Science Mathematics packages This metapackage will install Debian Science packages related to Mathematics. You might also be interested in the field::mathematics debtag and, depending on your focus, in the education-mathematics metapackage. Package: science-mathematics-dev Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: fflas-ffpack, libarmadillo-dev, libarpack2-dev, libatlas-base-dev, libblas-dev, libblitz0-dev, libcgal-dev, libcneartree-dev, libcqrlib2-dev, libcvector2-dev, libfreefem++-dev, libfreefem-dev, libgivaro-dev, libglpk-dev, libgsl0-dev, libhypre-dev, libitsol-dev, libjama-dev, liblapack-dev, liblip-dev, libmadlib-dev, libmatheval-dev, libmatio-dev, libmuparser-dev, libnewmat10-dev, libnglib-dev, libpolybori-dev, libpolybori-groebner-dev, libqd-dev, libranlip-dev, libscythestat-dev, libsparskit-dev, libspooles-dev, libstxxl-dev, libsuitesparse-dev, libsuperlu3-dev, libtnt-dev, petsc-dev, python-ffc, python-numpy, python-openopt, python-polybori, python-ufc, python-ufl, ufc Suggests: cfortran, fflas-ffpack-dev-doc, fflas-ffpack-user-doc, givaro-dev-doc, givaro-users-doc, libitpp-dev, liblevmar-dev, liblife-dev, liblrs-dev, libmei-dev, libmesh-dev, libnauty-dev, libopenturns-dev, libqrupdate-dev, libslepc3.0.0-dev, libtet1.4.2-dev, libtrilinos-dev, openturns-examples, python-openturns Description: Debian Science Mathematics-dev packages This metapackage will install Debian Science packages which might be helpful for development of applications for Mathematics. . You might also be interested in the science-mathematics metapackage. Package: science-meteorology Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: aweather, cdo, cmip5-cmor-tables, dballe, ecaccess, ferret-vis, freefoam, grads, libdap-bin, libdap-doc, libgrib-api-tools, magics++, nco, ncview, python-cmor, python-drslib, python-grib, vistrails, zygrib Suggests: geonetwork, gerris, gnudatalanguage, hdf-eos4, hdf-eos5, ncl, octave-octcdf, paraview, pydap, python-netcdf4, python-openturns, python-spherepack, r-base, visit Description: Debian Science Meteorology packages This metapackage is part of the Debian Pure Blend "Debian Science" and installs packages related to Meteorology and Climate. Package: science-meteorology-dev Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: libblas-dev, libblas-doc, libcmor-dev, libdap-dev, libemos-dev, libfftw3-dev, libfftw3-doc, libgadap-dev, libgctp-dev, libgrib-api-dev, libgrib-api-tools, libgrib2c-dev, libhe5-hdfeos-dev, liblapack-dev, liblapack-doc, liblas-dev, libnetcdf-dev, liboasis3-dev, libopenturns-dev, libproj-dev, librsl-dev, libterralib-dev, libudunits2-dev, netcdf-bin, openturns-examples, python-openturns, wcslib-dev, wcslib-doc Suggests: freefoam-dev, gfortran, ksh, libhe4-hdfeos-dev, liblife-dev, libspherepack-dev, pkg-config Description: Debian Science Meteorology-dev packages This metapackage will install Debian Science packages which might be helpful for development of applications for Meteorology and Climate. . You might also be interested in the science-meteorology metapackage. Package: science-nanoscale-physics Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: abinit, avogadro, axiom, cadabra, cp2k, drawxtl, etsf-io, extrema, feynmf, fityk, garlic, gdis, ggobi, ghemical, gnuplot, gperiodic, grace, graphviz, gsl-bin, gwyddion, libblacs-mpi1, libblas3gf, libfftw3-3, libgsl0ldbl, liblapack3gf, libscalapack-mpi1, maxima, mayavi2, mpqc, nco, ncview, netcdf-bin, netcdf-doc, openmpi-bin | mpich2, openmpi-doc | mpich2-doc, openmx, psi3, pymca, python-ase, python-scientific, python-scipy, python-scitools, python-sympy, pyxplot, qtoctave, quantum-espresso, science-numericalcomputation, v-sim Suggests: ape, atompaw, bigdft, dx, dx-doc, espresso++, exciting, fdmnes, gmsh, gpaw, gpiv, gpivtools, horae, ifeffit, life-apps, mpi-doc, mpich-bin, octaviz, octopus, python-elemental, qtiplot, scidavis, science-mathematics, science-statistics, scilab-sivp, sixpack, udav, wannier90 Description: Debian Science Nanoscale Physics packages This metapackage will install Debian Science packages related to Nanoscale Physics, which corresponds to the study of physical systems typically ranging from 1 to 100 nm in size. The properties of such systems usually depend on the number of atoms they are made of, while this number is still relatively large for an accurate description. . The nanoscale is the meeting point of classical and quantum physics. Previous research efforts were considering either smaller systems, for which everybody could develop their own methods and software independently, or much bigger systems, for which it was clearly impossible to provide a fine-grained description. Addressing the issues raised by the nanoscale requires however cooperative and coordinated efforts in a multidisciplinary context. This metapackage is part of such an endeavor. . You might also be interested in the debtag field::physics and, depending on your focus, in the physics and education-physics metapackages. Package: science-nanoscale-physics-dev Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: abinit-doc, gsl-bin, gsl-ref-html | gsl-ref-psdoc, libblacs-mpi-dev, libblas-dev, libblas-doc, libetsf-io-dev, libetsf-io-doc, libfftw3-dev, libfftw3-doc, libgsl0-dev, liblapack-dev, liblapack-doc, libnetcdf-dev, libroot-math-mlp-dev, libroot-montecarlo-vmc-dev, libroot-tmva-dev, libscalapack-mpi-dev, libxc-dev, netcdf-doc, root-system, scalapack-doc, science-mathematics-dev Suggests: gsl-doc-info, gsl-doc-pdf, libfox95, liblife-dev, libnbc, libopencascade-dev, libpspio, libtrilinos-dev, libtrilinos-doc, libxc, opencascade-draw, python-netcdf, spglib, wannier90-dev Description: Debian Science Nanoscale Physics development packages This metapackage will install Debian Science packages which might be helpful for the development of applications for Nanoscale Physics. . You might also be interested in the debtag field::physics and, depending on your focus, in the nanoscale-physics, physics and education-physics metapackages. Package: science-neuroscience-cognitive Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: amide, caret, dicom3tools, dicomnifti, itksnap, medcon, minc-tools, mriconvert, mricron, nifti-bin, openmeeg-tools, praat, psignifit, python-mvpa, python-nifti, python-pyepl, python-pypsignifit, python-pyxnat, python-statsmodels, voxbo, xmedcon Suggests: afni, bioimagesuite, brainvisa, connectomeviewer, debruijn, eeglab, fieldtrip, freesurfer, fsl, fslview, hid, iqr, lipsia, mni-autoreg, mni-n3, pysurfer, science-psychophysics, science-typesetting, slicer, spm8, xnat Description: Debian Science packages for Cognitive Neuroscience This metapackage will install Debian packages which might be useful for scientists doing cognitive neuroscience research. This comprises the full research process from conducting psychophysical experiments, over data acquisition and analysis, to visualization and typesetting of scientific results. . The selection of packages is targeting the application of analysis techniques. Methods developers are referred to the science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging, and med-imaging-dev metapackages for a variety of additional software that might be useful in the context of cognitive neuroscience. Package: science-neuroscience-modeling Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: cnrun, python-brian Suggests: invt, moose, nest, pcsim, pynn, xppaut Description: Debian Science packages for modeling of neural systems This metapackage will install Debian packages which might be useful for scientists interested in modeling of real neural systems at different levels (from single neuron to complex networks). . The selection of packages is targeting the application of simulation techniques. Methods developers are referred to the science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging, and med-imaging-dev metapackages for a variety of additional software that might be useful for neuroscience research. Package: science-numericalcomputation Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: esys-particle, freemat, gnudatalanguage, ipython, lammps, liggghts, lush, octave, pdl, python-deap, python-guiqwt, python-matplotlib, python-numpy, python-scipy, python-scitools, qtoctave, r-base, scilab, scilab-ann, scilab-scimax, scilab-sivp, scilab-swt, spyder, yade, yorick Suggests: hpcc, octavede Description: Debian Science Numerical Computation packages This metapackage will install Debian Science packages useful for numerical computation. The packages provide an array oriented calculation and visualisation system for scientific computing and data analysis. These packages are similar to commercial systems such as Matlab and IDL. Package: science-physics Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: abinit | mpqc | openmx | psi3, axiom, cadabra, cernlib, cp2k, drawxtl, etsf-io, feynmf, fityk, freefoam, geant321, gerris, ghkl, gpiv, gpivtools, gwyddion, libroot-math-mlp-dev, libroot-montecarlo-vmc-dev, libroot-tmva-dev, maxima, meshlab, opticalraytracer, paw, paw++, pymca, python-deap, python-sympy, quantum-espresso, root-system, science-electronics, science-numericalcomputation, tessa | tessa-mpi, v-sim Suggests: blzpack, clhep, espresso++, fdmnes, gate, geant4, horae, ifeffit, jfreemesh, liblife-dev, life-apps, octaviz, opencascade-draw, openfoam, paw-demos, science-mathematics, science-statistics, scilab-sivp, sixpack, spis Description: Debian Science Physics packages This metapackage will install Debian Science packages related to Physics. You might also be interested in the debtag field::physics and, depending on your focus, in education-physics metapackage. Package: science-physics-dev Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: pyfai Suggests: freefoam-dev Description: Debian Science Physics-dev packages This metapackage will install Debian Science packages which might be helpful for development of applications for Mathematics. . You might also be interested in the science-physics metapackage. Package: science-psychophysics Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: libfreenect-dev, octave-psychtoolbox-3, psychopy, python-pyepl, python-pyoptical Suggests: debruijn, nrec, opensesame, pebl, psychlops, psytoolkit, python-pyxid, science-bci, science-neuroscience-cognitive, tscope, visionegg Description: Debian Science packages for Psychophysics This metapackage will install Debian packages which might be useful for carrying out any experiment relating physical stimuli and their psychological effects. . The selection of packages is targeting software for stimuli delivery. For additional software related to the analysis of the acquired data refer to science-neuroscience-cognitive, med-imaging depending on the domain of application. Additionally look into science-bci since those often provide a complete loop frameworks including stimuli delivery. Package: science-robotics Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: gnuplot, libboost-dev, libcomedi0, libcv-dev, libode-dev, morse-simulator, octave, robot-player, rtai, xenomai-runtime Suggests: d-collide, libcoin60-runtime, libopenigtlink1, libvtk5.4, orca, orocos-bfl, orocos-kdl, orocos-ocl, orocos-rtt, roboop, rtnet, solid Description: Debian Robotics packages This metapackage is part of the Debian Pure Blend "Debian Science" and installs packages related to Robotics. . You might also be interested in the science-engineering metapackage. Package: science-simulations Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: esys-particle, freefoam, getdp, lammps, liggghts, python-deap, sumo, yade Suggests: fdmnes Description: Debian Science Simulation packages This metapackage will install Debian Science packages that are used to do simulations in different fields of science. Package: science-statistics Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: ess, littler, psignifit, python-openturns, python-scipy, python-statsmodels, r-cran-abind, r-cran-amore, r-cran-bayesm, r-cran-boot, r-cran-cairodevice, r-cran-car, r-cran-chron, r-cran-cluster, r-cran-coda, r-cran-codetools, r-cran-date, r-cran-dbi, r-cran-eco, r-cran-effects, r-cran-fbasics, r-cran-fcopulae, r-cran-fextremes, r-cran-fmultivar, r-cran-foptions, r-cran-foreign, r-cran-fportfolio, r-cran-gdata, r-cran-gmodels, r-cran-gplots, r-cran-gregmisc, r-cran-gtools, r-cran-hdf5, r-cran-hmisc, r-cran-its, r-cran-kernsmooth, r-cran-lattice, r-cran-latticeextra, r-cran-lme4, r-cran-lmtest, r-cran-mapdata, r-cran-mapproj, r-cran-maps, r-cran-matchit, r-cran-matrix, r-cran-mcmcpack, r-cran-mgcv, r-cran-misc3d, r-cran-mnp, r-cran-msm, r-cran-multcomp, r-cran-mvtnorm, r-cran-nlme, r-cran-psy, r-cran-qtl, r-cran-quadprog, r-cran-rcmdr, r-cran-relimp, r-cran-rggobi, r-cran-rgl, r-cran-rgtk2, r-cran-rmpi, r-cran-rms, r-cran-rmysql, r-cran-rodbc, r-cran-rpart, r-cran-rquantlib, r-cran-rserve, r-cran-rsprng, r-cran-sandwich, r-cran-sm, r-cran-snow, r-cran-strucchange, r-cran-survival, r-cran-teachingdemos, r-cran-tkrplot, r-cran-tseries, r-cran-vcd, r-cran-vgam, r-cran-xml, r-cran-zelig, r-cran-zoo, r-recommended, rkward Suggests: pandas, python-stats, r-cran-acepack, r-cran-fcalendar, r-cran-fecofin, r-cran-fseries, r-cran-rmetrics, r-cran-rpvm, r-cran-spc, r-cran-vr, r-other-gking-matchit, science-mathematics Description: Debian Science Statistics packages This metapackage is part of the Debian Pure Blend "Debian Science" and installs packages related to statistics. This task is a general task which might be useful for any scientific work. It depends from a lot of R packages as well as from other tools which are useful to do statistics. Moreover the Science Mathematics task is suggested to optionally install all mathematics related software. Package: science-typesetting Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: auctex, biber, bibus, bibutils, cb2bib, dia, diploma, feynmf, impose+, jabref, jeuclid-mathviewer, kbibtex, latexdiff, libjlatexmath-java, lyx, mlpost, pybliographer, referencer, sketch, texlive, texlive-bibtex-extra, texlive-math-extra, texlive-publishers, texlive-science, texmacs, texmacs-extra-fonts, transfig, xfig Suggests: csv2latex, gpapers, libgtkmathview-bin, openoffice.org-dmaths, pymarc, quaneko, r-cran-xtable, tellico, texmaker, zotero Description: Debian Science typesetting packages This metapackage will install Debian Science packages related to typesetting. You might also be interested in the use::typesetting debtag. Package: science-viewing Architecture: all Depends: science-tasks (= ${binary:Version}), science-config (= ${binary:Version}) Recommends: 3depict, fityk, g3data, gle-graphics, gmsh, gnudatalanguage, gnuplot, grace, graphviz, gri, gwyddion, ifrit, imview, kst, lybniz, mathgl, matlab2tikz, mayavi2, paraview, pdl, plotdrop, python-guiqwt, python-scientific, python-viper, pyxplot, qtiplot, vistrails, yorick Suggests: cassandra, circos, findimagedupes, grits, jeuclid-mathviewer, labplot, libgtkmathview-bin, libpuzzle-bin, med-imaging, pgfplots, pgplot5, python-matplotlib, python-scitools, r-cran-aplpack, r-cran-colorspace, r-cran-plotrix, texlive-pictures, udav, visit Description: Debian Science data visualisation packages This metapackage will install Debian Science packages related to data visualization. You might also be interested in the use::viewing debtag. debian-science-1.0ubuntu1/debian/rules0000755000000000000000000000007011360134132014706 0ustar #!/usr/bin/make -f include /usr/share/blends-dev/rules debian-science-1.0ubuntu1/menu/0000755000000000000000000000000011360134132013353 5ustar debian-science-1.0ubuntu1/menu/electronics/0000755000000000000000000000000011360134132015665 5ustar debian-science-1.0ubuntu1/menu/typesetting/0000755000000000000000000000000011360134132015732 5ustar debian-science-1.0ubuntu1/menu/statistics/0000755000000000000000000000000011360134132015545 5ustar debian-science-1.0ubuntu1/menu/viewing/0000755000000000000000000000000011360134132015023 5ustar debian-science-1.0ubuntu1/menu/mathematics/0000755000000000000000000000000011360134132015652 5ustar debian-science-1.0ubuntu1/menu/astronomy/0000755000000000000000000000000011360134132015406 5ustar debian-science-1.0ubuntu1/menu/biology/0000755000000000000000000000000011360134132015017 5ustar debian-science-1.0ubuntu1/menu/geography/0000755000000000000000000000000011360134132015340 5ustar debian-science-1.0ubuntu1/menu/chemistry/0000755000000000000000000000000011360134132015362 5ustar debian-science-1.0ubuntu1/menu/physics/0000755000000000000000000000000011360134132015035 5ustar debian-science-1.0ubuntu1/debian-science-tasks.desc0000644000000000000000000007456012264702434017251 0ustar Task: science-astronomy Section: debian-science Description: Debian Science Astronomy packages This metapackage will install Debian Science packages related to Astronomy. You might also be interested in field::astronomy debtag and, depending on your focus, in the education-astronomy metapackage. Relevance: 10 Key: science-astronomy Packages: list gcx astronomical-almanac lightspeed openuniverse sextractor wcstools wcslib-tools funtools esorex gpredict predict qfits-tools yorick-full savi stellarium xplanet lynkeos.app stardata-common boinc-app-milkyway boinc-app-seti gyoto ftools-fv saods9 Task: science-astronomy-dev Section: debian-science Description: Debian Science Astronomy-dev packages This metapackage will install Debian Science packages which might be helpful for development of applications for Astronomy. . You might also be interested in the science-astronomy metapackage. Relevance: 10 Key: science-astronomy-dev Packages: list libnova-dev libccfits-dev libcfitsio3-dev python-pyfits libqfits-dev slang-cfitsio libastro-fits-cfitsio-perl libsofa-c-dev libstarlink-pal-dev libstarlink-ast-dev libwcstools-dev wcslib-dev libcpl-dev python-pywcs python-cpl Task: science-bci Section: debian-science Description: Debian Science packages for the design and use of brain-computer interface (BCI) -- direct communication pathway between a brain and an external device. BCIs are often aimed at assisting, augmenting or repairing human cognitive or sensory-motor functions. . The selection of packages is targeting the complete frameworks for the design of BCI systems. Often such systems rely on external presentation, data collection and analysis software which could be found in science-neuroscience-cognitive, science-dataacquisition, data-machine-learning metapackages. Relevance: 10 Packages: list Task: science-biology Section: debian-science Description: Debian Science Biology packages This metapackage will install Debian Science packages related to Biology. You might also be interested in the field::biology debtag. . This metapackage makes use of the packages med-bio and med-bio-dev (for development of biological applications) which are maintained by Debian Med - another Debian Pure Blend. If you are a biologist you are most probably interested in the Debian Med project which deals with biology and medicine in much more detail then the more general Debian Science. Relevance: 10 Key: science-biology Packages: list med-bio bauble critterding Task: science-chemistry Section: debian-science Description: Debian Science Chemistry packages This metapackage will install Debian Science packages related to Chemistry. You might also be interested in the field::chemistry debtag and, depending on your focus, in the education-chemistry metapackage. Relevance: 10 Key: science-chemistry Packages: list apbs bkchem bodr libcdk-java chemeq chemical-mime-data chemtool easychem gabedit galculator garlic gausssum gchempaint gdis ghemical gcrystal gcu-bin gcu-plugin gperiodic gromacs kalzium katomic mopac7-bin mpqc mpqc-support openbabel python-openbabel psi3 pymol viewmol xdrawchem xmakemol-gl v-sim rasmol adun.app gdpc xbs gelemental avogadro gamgi massxpert drawxtl chemical-structures freefoam pyfai jmol qutemol cp2k pdb2pqr mmass mmass-modules python-mzml tandem-mass Task: science-dataacquisition Section: debian-science Description: Debian Science data acquisition packages This metapackage will install Debian Science packages related to data acquisition. This might be used in several sciences (as for instance science-viewing and science-typesetting). Relevance: 10 Key: science-dataacquisition Packages: list engauge-digitizer g3data netcdf-bin jaaa ghkl libfreenect-dev Task: science-distributedcomputing Section: debian-science Description: Debian Science Distributed Computing packages This metapackage will install Debian Science packages useful for various types of distributed computing, such as grid-, cloud-, cluster- and parallel-computing. Relevance: 10 Key: science-distributedcomputing Packages: list ipython torque-common torque-server libarccommon2 gridengine-client gridengine-exec gridengine-master gridengine-qmon globus-core openmpi-bin mpich2 openmpipython mpich2python python-mpi condor dmtcp environment-modules Task: science-electronics Section: debian-science Description: Debian Science Electronics packages This metapackage will install Debian Science packages related to Electronics. You might also be interested in the field::electronics debtag and, depending on your focus, in the education-electronics metapackage. Relevance: 10 Key: science-electronics Packages: list avrdude gcc-avr gerbv uisp electric geda kicad freehdl iverilog verilator gplcver gputils simulpic pcb oregano tkgate texlive-latex-extra linsmith xsmc-calc confluence gspiceui gnucap qelectrotech covered arduino arduino-core visolate fritzing Task: science-electrophysiology Section: debian-science Description: Debian Science packages for Electrophysiology This metapackage will install Debian packages which might be useful for scientists doing electrophysiology-based neuroscience research. . The selection of packages is targeting the application of analysis techniques. Methods developers are referred to the science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging, and med-imaging-dev metapackages for a variety of additional software that might be useful for electrophysiology research. Relevance: 10 Key: science-electrophysiology Packages: list libgdf-dev sigviewer libdrawtk-dev Task: science-engineering Section: debian-science Description: Debian Science Engineering packages This metapackage is part od the Debian Pure Blend "Debian Science" and installs packages related to Engineering. . Please not that there is an additional package engineering-dev which depends from packages which are useful to develop engineering related software. Relevance: 10 Key: science-engineering Packages: list librecad sailcut python-silo libsilo-bin gerris gmsh getdp netgen pythoncad z88 freecad python-openturns code-aster-gui code-saturne hdfview cba python-fiat syrthes freefoam cgns-convert Task: science-engineering-dev Section: debian-science Description: Debian Science Engineering-dev packages This metapackage will install Debian Science packages which might be helpful for development of applications for Engineering. . You might also be interested in the science-engineering metapackage. Relevance: 10 Key: science-engineering-dev Packages: list libalberta2-dev libcgns-dev libitpp-dev libexodusii-dev libadios-dev libbox-dev libsilo-dev libxdmf-dev libgetfem++-dev libhdf5-serial-dev libjhdf5-java libjhdf4-java libopenturns-dev libmadlib-dev libelmer-dev libmed-dev libmedc-dev libmedimport-dev libnetcdf-dev python-netcdf syfi-dev Task: science-geography Section: debian-science Description: Debian Science Geography packages This metapackage will install Debian Science packages related to Geography. You might also be interested in the field::geography debtag and, depending on your focus, in the education-geography metapackage. Relevance: 10 Key: science-geography Packages: list gis-workstation grass qgis qgis-plugin-grass proj-bin mapserver-bin gmt gpsbabel gpx2shp gpsd gpsdrive gpsman openscenegraph thuban drawmap gpstrans geoip-bin gpsd-clients grass-doc php5-mapscript phppgadmin gpsmanshp viking avce00 e00compr gdal-bin ogdi-bin postgis osm2pgsql josm josm-plugins merkaartor gosmore python-mapnik2 mapnik-utils osmpbf-bin imposm r-cran-sp r-cran-mapdata r-cran-mapproj r-cran-maps pgadmin3 Task: science-highenergy-physics Section: debian-science Description: Debian Science High Energy Physics packages This metapackage will install Debian Science packages related to High Energy Physics, which is a branch of physics that studies the elementary subatomic constituents of matter and radiation, and their interactions. The field is also called Particle Physics. . You might also be interested in the debtag field::physics and, depending on your focus, in the physics and education-physics metapackages. Relevance: 10 Key: science-highenergy-physics Packages: list cernlib cernlib-base cernlib-core cernlib-extras dzedit kuipc kxterm nypatchy pawserv zftp paw paw++ cernlib-montecarlo geant321 feynmf looptools python-lhapdf octave-lhapdf root-macro-fastjet pythia8-root-interface libroot-bindings-python5.34 libroot-bindings-ruby5.34 libroot-graf3d-gl5.34 libroot-io-xmlparser5.34 libroot-math-mathmore5.34 libroot-math-unuran5.34 libroot-misc-memstat5.34 libroot-misc-table5.34 libroot-net-bonjour5.34 libroot-net-ldap5.34 libroot-roofit5.34 libroot-geom5.34 libroot-graf2d-gpad5.34 libroot-graf2d-graf5.34 libroot-graf2d-postscript5.34 libroot-graf3d-eve5.34 libroot-graf3d-g3d5.34 libroot-gui5.34 libroot-gui-ged5.34 libroot-hist5.34 libroot-hist-spectrum5.34 libroot-html5.34 libroot-io5.34 libroot-math-foam5.34 libroot-math-genvector5.34 libroot-math-mathcore5.34 libroot-math-matrix5.34 libroot-math-minuit5.34 libroot-math-mlp5.34 libroot-math-physics5.34 libroot-math-quadp5.34 libroot-math-smatrix5.34 libroot-math-splot5.34 libroot-misc-minicern5.34 libroot-montecarlo-eg5.34 libroot-montecarlo-vmc5.34 libroot-net5.34 libroot-net-auth5.34 libroot-proof5.34 libroot-proof-proofplayer5.34 libroot-tmva5.34 libroot-tree5.34 libroot-tree-treeplayer5.34 libroot-core5.34 root-plugin-graf2d-asimage root-plugin-geom-gdml root-plugin-gui-qt root-plugin-graf2d-qt root-plugin-math-fftw3 root-plugin-math-minuit2 root-plugin-montecarlo-pythia8 root-plugin-net-globus root-plugin-net-krb5 root-plugin-sql-mysql root-plugin-sql-odbc root-plugin-sql-pgsql root-plugin-geom-geombuilder root-plugin-geom-geompainter root-plugin-graf2d-x11 root-plugin-graf3d-x3d root-plugin-gui-fitpanel root-plugin-gui-guibuilder root-plugin-gui-sessionviewer root-plugin-hist-hbook root-plugin-hist-histpainter root-plugin-hist-spectrumpainter root-plugin-io-sql root-plugin-io-xml root-plugin-math-fumili root-plugin-tree-treeviewer root-system-proofd root-system-rootd root-system-bin root-system-common root-system rivet rivet-plugins python-rivet rivet-root-converter thepeg thepeg-gui herwig++ Task: science-highenergy-physics-dev Section: debian-science Description: Debian Science High Energy Physics development packages This metapackage will install Debian Science packages related to development of High Energy Physics applications, which is a branch of physics that studies the elementary subatomic constituents of matter and radiation, and their interactions. The field is also called Particle Physics. . You might also be interested in the debtag field::physics and, depending on your focus, in the physics and education-physics metapackages. Relevance: 10 Key: science-highenergy-physics-dev Packages: list cernlib-base-dev cernlib-core-dev libclhep-dev libhepmc-dev libhepmcfio-dev liblhapdf-dev libsiscone-dev libsiscone-spherical-dev libfastjet-dev libfastjettools-dev libfastjet-fortran-dev libfastjetplugins-dev libpythia8-dev fcc libooptools-dev libroot-bindings-python-dev libroot-bindings-ruby-dev libroot-graf3d-gl-dev libroot-io-xmlparser-dev libroot-math-mathmore-dev libroot-math-unuran-dev libroot-misc-memstat-dev libroot-misc-table-dev libroot-net-bonjour-dev libroot-net-ldap-dev libroot-roofit-dev libroot-geom-dev libroot-graf2d-gpad-dev libroot-graf2d-graf-dev libroot-graf2d-postscript-dev libroot-graf3d-eve-dev libroot-graf3d-g3d-dev libroot-gui-dev libroot-gui-ged-dev libroot-hist-dev libroot-hist-spectrum-dev libroot-html-dev libroot-io-dev libroot-math-foam-dev libroot-math-genvector-dev libroot-math-mathcore-dev libroot-math-matrix-dev libroot-math-minuit-dev libroot-math-mlp-dev libroot-math-physics-dev libroot-math-quadp-dev libroot-math-smatrix-dev libroot-math-splot-dev libroot-misc-minicern-dev libroot-montecarlo-eg-dev libroot-montecarlo-vmc-dev libroot-net-dev libroot-net-auth-dev libroot-proof-dev libroot-proof-proofplayer-dev libroot-tmva-dev libroot-tree-dev libroot-tree-treeplayer-dev libroot-core-dev libroot-static librivet-dev rivet-plugins-dev libthepeg-dev herwig++-dev Task: science-imageanalysis Section: debian-science Description: Debian Science image analysis packages This metapackage will install Debian Science packages related to scientific image acquisition. This might be used in several sciences (as for instance science-dataacquisition, science-viewing and science-typesetting). Relevance: 10 Key: science-imageanalysis Packages: list gpivtools gpiv libcv-dev gwyddion libteem2 Task: science-linguistics Section: debian-science Description: Debian Science Linguistics packages This metapackage is part of the Debian Pure Blend "Debian Science" and installs packages related to Linguistics. Relevance: 10 Key: science-linguistics Packages: list wordnet apertium link-grammar artha timbl timblserver mbt mbtserver ucto dimbl frog Task: science-machine-learning Section: debian-science Description: Debian Science Machine Learning packages This metapackage will install Debian packages which might be useful for scientists interested in machine learning. Included packages range from knowledge-based (expert) inference systems to software implementing dominant nowadays statistical methods. Relevance: 10 Key: science-machine-learning Packages: list python-pyke gprolog yap libtorch3-dev libshogun-dev libfann-dev libsvm-dev liblinear-dev libocas-dev python-scikits-learn python-mdp python-mlpy weka vowpal-wabbit r-cran-mass r-cran-bayesm r-cran-class r-cran-cluster r-cran-msm r-cran-mcmcpack r-cran-mnp r-cran-amore python-mvpa python-statsmodels root-system libroot-tmva-dev libroot-montecarlo-vmc-dev libroot-math-mlp-dev autoclass mcl scilab-ann libga-dev libevocosm-dev pgapack python-genetic octave-ga python-pyevolve lush libcv-dev python-opencv libvigraimpex-dev python-vigra python-pebl python-pymc Task: science-mathematics Section: debian-science Description: Debian Science Mathematics packages This metapackage will install Debian Science packages related to Mathematics. You might also be interested in the field::mathematics debtag and, depending on your focus, in the education-mathematics metapackage. Relevance: 10 Key: science-mathematics Packages: list axiom ginac-tools xmaxima wxmaxima pari-gp pari-extra gap gerris freefem freefem3d freefem++ netgen gmsh getdp coq proofgeneral matita agda prover9 hol-light minisat science-statistics ess littler r-recommended rkward r-cran-mapproj r-cran-abind r-cran-bayesm r-cran-boot r-cran-cairodevice r-cran-car r-cran-chron r-cran-cluster r-cran-coda r-cran-codetools r-cran-date r-cran-dbi r-cran-rms r-cran-eco r-cran-effects r-cran-fbasics r-cran-fcopulae r-cran-fextremes r-cran-fmultivar r-cran-foptions r-cran-foreign r-cran-fportfolio r-cran-gdata r-cran-gmodels r-cran-gplots r-cran-gregmisc r-cran-gtools r-cran-hdf5 r-cran-hmisc r-cran-its r-cran-kernsmooth r-cran-lattice r-cran-latticeextra r-cran-lme4 r-cran-lmtest r-cran-mapdata r-cran-maps r-cran-matchit r-cran-matrix r-cran-mcmcpack r-cran-mgcv r-cran-misc3d r-cran-mnp r-cran-multcomp r-cran-mvtnorm r-cran-nlme r-cran-psy r-cran-qtl r-cran-quadprog r-cran-rcmdr r-cran-relimp r-cran-rggobi r-cran-rgl r-cran-rgtk2 r-cran-rmpi r-cran-rmysql r-cran-rodbc r-cran-rpart r-cran-rquantlib r-cran-rserve r-cran-rsprng r-cran-sandwich r-cran-sm r-cran-snow r-cran-strucchange r-cran-survival r-cran-tkrplot r-cran-tseries r-cran-vgam r-cran-xml r-cran-zelig r-cran-zoo r-cran-msm r-cran-amore r-cran-teachingdemos psignifit python-scipy r-cran-vcd python-statsmodels python-openturns geomview octave xmds freemat mathomatic scilab scilab-sivp scilab-scimax scilab-swt scilab-ann regina-normal snappea lp-solve libmatheval1 mumps-test geogebra lrslib python-ffc polylib-utils rheolef scotch bliss qtoctave python-deap mcl polybori-gui polybori Task: science-mathematics-dev Section: debian-science Description: Debian Science Mathematics-dev packages This metapackage will install Debian Science packages which might be helpful for development of applications for Mathematics. . You might also be interested in the science-mathematics metapackage. Relevance: 10 Key: science-mathematics-dev Packages: list libnglib-dev python-numpy libgsl0-dev liblapack-dev libatlas-base-dev libblas-dev libsuperlu3-dev libglpk-dev libcgal-dev libmatheval-dev python-openopt libmatio-dev libblitz0-dev libjama-dev libtnt-dev liblip-dev libranlip-dev libarpack2-dev libarmadillo-dev libstxxl-dev libnewmat10-dev libmadlib-dev petsc-dev libqd-dev libcqrlib2-dev libcvector2-dev libhypre-dev libitsol-dev libmuparser-dev libcneartree-dev libsparskit-dev libspooles-dev libsuitesparse-dev ufc python-ufc python-ffc python-ufl libscythestat-dev libfreefem++-dev libfreefem-dev libgivaro-dev fflas-ffpack libpolybori-dev libpolybori-groebner-dev python-polybori Task: science-meteorology Section: debian-science Description: Debian Science Meteorology packages This metapackage is part of the Debian Pure Blend "Debian Science" and installs packages related to Meteorology and Climate. Relevance: 10 Key: science-meteorology Packages: list cdo nco dballe zygrib ncview grads ferret-vis magics++ freefoam libgrib-api-tools ecaccess python-grib python-drslib python-cmor cmip5-cmor-tables aweather libdap-bin libdap-doc vistrails Task: science-meteorology-dev Section: debian-science Description: Debian Science Meteorology-dev packages This metapackage will install Debian Science packages which might be helpful for development of applications for Meteorology and Climate. . You might also be interested in the science-meteorology metapackage. Relevance: 10 Key: science-meteorology-dev Packages: list libemos-dev libgadap-dev libcmor-dev libgrib-api-dev libgrib-api-tools libgrib2c-dev libhe5-hdfeos-dev libproj-dev libgctp-dev libnetcdf-dev netcdf-bin liblapack-dev libblas-dev libfftw3-dev libblas-doc liblapack-doc libfftw3-doc liblas-dev libterralib-dev liboasis3-dev libudunits2-dev libdap-dev python-openturns libopenturns-dev openturns-examples wcslib-dev wcslib-doc librsl-dev Task: science-nanoscale-physics Section: debian-science Description: Debian Science Nanoscale Physics packages This metapackage will install Debian Science packages related to Nanoscale Physics, which corresponds to the study of physical systems typically ranging from 1 to 100 nm in size. The properties of such systems usually depend on the number of atoms they are made of, while this number is still relatively large for an accurate description. . The nanoscale is the meeting point of classical and quantum physics. Previous research efforts were considering either smaller systems, for which everybody could develop their own methods and software independently, or much bigger systems, for which it was clearly impossible to provide a fine-grained description. Addressing the issues raised by the nanoscale requires however cooperative and coordinated efforts in a multidisciplinary context. This metapackage is part of such an endeavor. . You might also be interested in the debtag field::physics and, depending on your focus, in the physics and education-physics metapackages. Relevance: 10 Key: science-nanoscale-physics Packages: list abinit mpqc openmx psi3 quantum-espresso drawxtl etsf-io feynmf fityk gnuplot grace libblas3gf liblapack3gf libfftw3-3 libgsl0ldbl gsl-bin netcdf-bin netcdf-doc nco ncview openmpi-bin openmpi-doc science-numericalcomputation octave python-matplotlib python-scipy ipython python-numpy spyder python-guiqwt pdl gnudatalanguage scilab scilab-sivp scilab-scimax scilab-swt scilab-ann freemat yorick r-base qtoctave lush yade liggghts esys-particle python-scitools python-deap lammps avogadro garlic gdis ghemical v-sim gwyddion cp2k pymca python-ase axiom maxima cadabra extrema ggobi mayavi2 udav gperiodic python-elemental graphviz libblacs-mpi1 libscalapack-mpi1 python-scientific python-sympy pyxplot Task: science-nanoscale-physics-dev Section: debian-science Description: Debian Science Nanoscale Physics development packages This metapackage will install Debian Science packages which might be helpful for the development of applications for Nanoscale Physics. . You might also be interested in the debtag field::physics and, depending on your focus, in the nanoscale-physics, physics and education-physics metapackages. Relevance: 10 Key: science-nanoscale-physics-dev Packages: list abinit-doc libblas-dev libblas-doc liblapack-dev liblapack-doc libetsf-io-dev libetsf-io-doc libfftw3-dev libfftw3-doc libgsl0-dev gsl-bin gsl-ref-html libnetcdf-dev netcdf-doc libxc-dev root-system libroot-tmva-dev libroot-montecarlo-vmc-dev libroot-math-mlp-dev gsl-doc-pdf libblacs-mpi-dev libscalapack-mpi-dev scalapack-doc science-mathematics-dev libnglib-dev python-numpy libatlas-base-dev libsuperlu3-dev libglpk-dev libcgal-dev libmatheval-dev python-openopt libmatio-dev libblitz0-dev libjama-dev libtnt-dev liblip-dev libranlip-dev libarpack2-dev libarmadillo-dev libstxxl-dev libnewmat10-dev libmadlib-dev petsc-dev libqd-dev libcqrlib2-dev libcvector2-dev libhypre-dev libitsol-dev libmuparser-dev libcneartree-dev libsparskit-dev libspooles-dev libsuitesparse-dev ufc python-ufc python-ffc python-ufl libscythestat-dev libfreefem++-dev libfreefem-dev libgivaro-dev fflas-ffpack libpolybori-dev libpolybori-groebner-dev python-polybori Task: science-neuroscience-cognitive Section: debian-science Description: Debian Science packages for Cognitive Neuroscience This metapackage will install Debian packages which might be useful for scientists doing cognitive neuroscience research. This comprises the full research process from conducting psychophysical experiments, over data acquisition and analysis, to visualization and typesetting of scientific results. . The selection of packages is targeting the application of analysis techniques. Methods developers are referred to the science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging, and med-imaging-dev metapackages for a variety of additional software that might be useful in the context of cognitive neuroscience. Relevance: 10 Key: science-neuroscience-cognitive Packages: list psignifit amide dicomnifti minc-tools medcon xmedcon nifti-bin python-nifti python-mvpa caret python-pyepl praat dicom3tools voxbo openmeeg-tools mricron itksnap python-pypsignifit python-statsmodels mriconvert python-pyxnat Task: science-neuroscience-modeling Section: debian-science Description: Debian Science packages for modeling of neural systems This metapackage will install Debian packages which might be useful for scientists interested in modeling of real neural systems at different levels (from single neuron to complex networks). . The selection of packages is targeting the application of simulation techniques. Methods developers are referred to the science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging, and med-imaging-dev metapackages for a variety of additional software that might be useful for neuroscience research. Relevance: 10 Key: science-neuroscience-modeling Packages: list python-brian cnrun Task: science-numericalcomputation Section: debian-science Description: Debian Science Numerical Computation packages This metapackage will install Debian Science packages useful for numerical computation. The packages provide an array oriented calculation and visualisation system for scientific computing and data analysis. These packages are similar to commercial systems such as Matlab and IDL. Relevance: 10 Key: science-numericalcomputation Packages: list octave python-matplotlib python-scipy ipython python-numpy spyder python-guiqwt pdl gnudatalanguage scilab scilab-sivp scilab-scimax scilab-swt scilab-ann freemat yorick r-base qtoctave lush yade liggghts esys-particle python-scitools python-deap lammps Task: science-physics Section: debian-science Description: Debian Science Physics packages This metapackage will install Debian Science packages related to Physics. You might also be interested in the debtag field::physics and, depending on your focus, in education-physics metapackage. Relevance: 10 Key: science-physics Packages: list cernlib geant321 paw++ paw abinit gerris feynmf freefoam fityk tessa science-numericalcomputation octave python-matplotlib python-scipy ipython python-numpy spyder python-guiqwt pdl gnudatalanguage scilab scilab-sivp scilab-scimax scilab-swt scilab-ann freemat yorick r-base qtoctave lush yade liggghts esys-particle python-scitools python-deap lammps science-electronics avrdude gcc-avr gerbv uisp electric geda kicad freehdl iverilog verilator gplcver gputils simulpic pcb oregano tkgate texlive-latex-extra linsmith xsmc-calc confluence gspiceui gnucap qelectrotech covered arduino arduino-core visolate fritzing v-sim gpiv gpivtools maxima python-sympy axiom meshlab cadabra drawxtl opticalraytracer ghkl etsf-io pymca quantum-espresso gwyddion cp2k root-system libroot-tmva-dev libroot-montecarlo-vmc-dev libroot-math-mlp-dev Task: science-physics-dev Section: debian-science Description: Debian Science Physics-dev packages This metapackage will install Debian Science packages which might be helpful for development of applications for Mathematics. . You might also be interested in the science-physics metapackage. Relevance: 10 Key: science-physics-dev Packages: list pyfai Task: science-psychophysics Section: debian-science Description: Debian Science packages for Psychophysics This metapackage will install Debian packages which might be useful for carrying out any experiment relating physical stimuli and their psychological effects. . The selection of packages is targeting software for stimuli delivery. For additional software related to the analysis of the acquired data refer to science-neuroscience-cognitive, med-imaging depending on the domain of application. Additionally look into science-bci since those often provide a complete loop frameworks including stimuli delivery. Relevance: 10 Key: science-psychophysics Packages: list psychopy python-pyoptical python-pyepl libfreenect-dev octave-psychtoolbox-3 Task: science-robotics Section: debian-science Description: Debian Robotics packages This metapackage is part of the Debian Pure Blend "Debian Science" and installs packages related to Robotics. . You might also be interested in the science-engineering metapackage. Relevance: 10 Key: science-robotics Packages: list rtai xenomai-runtime libcv-dev libcomedi0 octave gnuplot libboost-dev libode-dev morse-simulator robot-player Task: science-simulations Section: debian-science Description: Debian Science Simulation packages This metapackage will install Debian Science packages that are used to do simulations in different fields of science. Relevance: 10 Key: science-simulations Packages: list sumo esys-particle lammps liggghts yade python-deap freefoam getdp Task: science-statistics Section: debian-science Description: Debian Science Statistics packages This metapackage is part of the Debian Pure Blend "Debian Science" and installs packages related to statistics. This task is a general task which might be useful for any scientific work. It depends from a lot of R packages as well as from other tools which are useful to do statistics. Moreover the Science Mathematics task is suggested to optionally install all mathematics related software. Relevance: 10 Key: science-statistics Packages: list ess littler r-recommended rkward r-cran-mapproj r-cran-abind r-cran-bayesm r-cran-boot r-cran-cairodevice r-cran-car r-cran-chron r-cran-cluster r-cran-coda r-cran-codetools r-cran-date r-cran-dbi r-cran-rms r-cran-eco r-cran-effects r-cran-fbasics r-cran-fcopulae r-cran-fextremes r-cran-fmultivar r-cran-foptions r-cran-foreign r-cran-fportfolio r-cran-gdata r-cran-gmodels r-cran-gplots r-cran-gregmisc r-cran-gtools r-cran-hdf5 r-cran-hmisc r-cran-its r-cran-kernsmooth r-cran-lattice r-cran-latticeextra r-cran-lme4 r-cran-lmtest r-cran-mapdata r-cran-maps r-cran-matchit r-cran-matrix r-cran-mcmcpack r-cran-mgcv r-cran-misc3d r-cran-mnp r-cran-multcomp r-cran-mvtnorm r-cran-nlme r-cran-psy r-cran-qtl r-cran-quadprog r-cran-rcmdr r-cran-relimp r-cran-rggobi r-cran-rgl r-cran-rgtk2 r-cran-rmpi r-cran-rmysql r-cran-rodbc r-cran-rpart r-cran-rquantlib r-cran-rserve r-cran-rsprng r-cran-sandwich r-cran-sm r-cran-snow r-cran-strucchange r-cran-survival r-cran-tkrplot r-cran-tseries r-cran-vgam r-cran-xml r-cran-zelig r-cran-zoo r-cran-msm r-cran-amore r-cran-teachingdemos psignifit python-scipy r-cran-vcd python-statsmodels python-openturns Task: science-typesetting Section: debian-science Description: Debian Science typesetting packages This metapackage will install Debian Science packages related to typesetting. You might also be interested in the use::typesetting debtag. Relevance: 10 Key: science-typesetting Packages: list referencer kbibtex impose+ pybliographer texlive-bibtex-extra jabref bibutils biber feynmf texlive texlive-science texlive-publishers texlive-math-extra diploma lyx texmacs texmacs-extra-fonts auctex xfig transfig dia bibus mlpost latexdiff libjlatexmath-java cb2bib jeuclid-mathviewer sketch Task: science-viewing Section: debian-science Description: Debian Science data visualisation packages This metapackage will install Debian Science packages related to data visualization. You might also be interested in the use::viewing debtag. Relevance: 10 Key: science-viewing Packages: list vistrails pdl gnudatalanguage kst ifrit yorick python-scientific fityk gnuplot grace gri graphviz pyxplot plotdrop qtiplot python-guiqwt imview mayavi2 g3data gwyddion paraview gle-graphics gmsh lybniz 3depict mathgl python-viper matlab2tikz debian-science-1.0ubuntu1/Makefile0000755000000000000000000000007311360134132014052 0ustar #!/usr/bin/make -f include /usr/share/blends-dev/Makefile debian-science-1.0ubuntu1/tasks/0000755000000000000000000000000012264701150013540 5ustar debian-science-1.0ubuntu1/tasks/electronics0000644000000000000000000000757211722223577016022 0ustar Task: Electronics Description: Debian Science Electronics packages This metapackage will install Debian Science packages related to Electronics. You might also be interested in the field::electronics debtag and, depending on your focus, in the education-electronics metapackage. Depends: avrdude, gcc-avr, gerbv, qucs, uisp Depends: electric Depends: geda Suggests: geda-examples, geda-doc Depends: kicad Suggests: kicad-doc-de, kicad-doc-en, kicad-doc-es, kicad-doc-fr, \ kicad-doc-it, kicad-doc-pt, kicad-doc-ru Depends: freehdl, ghdl, iverilog, verilator, gplcver Why: VHDL Depends: klogic Depends: gputils, simulpic Why: PIC Depends: pcb Why: PCB Depends: oregano Depends: tkgate Depends: texlive-latex-extra Why: contains circ-tex and circ-tex has a grave bug which makes \ science-electronics uninstallable on several machines Depends: linsmith, xsmc-calc Why: Smith charts Depends: confluence Depends: ngspice, gspiceui, easyspice Depends: gnucap Depends: qelectrotech Depends: covered Depends: arduino, arduino-core Depends: herb WNPP: 516928 Homepage: http://www.banu.com/herb License: GNU GPLv3 Responsible: أحمد المحمودي (Ahmed El-Mahmoudy) Pkg-Description: complete set of CAD programs for design of VLSI circuits Herb is a complete set of CAD programs and libraries for the specification, design and validation of VLSI circuits. It includes a VHDL simulator, logic synthesis tools, automatic place and route tools, layout editors, portable CMOS standard cell libraries and custom block generators for creating custom high performance circuits. . Herb supports the following file formats: * Behavioural: VHDL, VHDL FSM (input-only) * Netlists: Alliance, SPICE, EDIF 2.0, VHDL, COMPASS, HILO (output-only) and Verilog (output-only) * Symbolic layout: Alliance, COMPASS * Physical layout: CIF (output-only) and GDSII (output-only) Suggests: liblife-dev Why: Partial differential equations library, FEA, CFD Depends: visolate Depends: fritzing Depends: vbpp Pkg-URL: http://snapshot.debian.org/package/vbpp/ Homepage: http://www.flex.com/~jching/ Pkg-Description: Verilog preprocessor VBPP is a Verilog preprocessor. It has support for most Verilog preprocessing directives and additional directives such as: . * Statement generator ('generate' command in VHDL). * Expression evaluation. * Mathematical functions: log2, ceil, floor, round, abs, etc. * Conditionals: if, switch, etc. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/324765 Depends: vbs Pkg-URL: http://snapshot.debian.org/package/vbs/ Homepage: http://www.flex.com/~jching/ Pkg-Description: Verilog Behavioral Simulation Verilog is a Hardware Description Language used mostly for digital circuit design and simulation. This program is a simple implementation of a Verilog simulator. VBS tries to implement all of the Verilog behavioral constructs that are synthesizable, but still allow complex test vectors for simulation. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/303625 Depends: ksimus Pkg-URL: http://snapshot.debian.org/package/ksimus/ Homepage: http://ksimus.berlios.de Pkg-Description: KDE tool for simulating electrical circuits KSimus is an application for simulating networks with boolean and floating point data type. Some more data types are planned. Currently there exists only a few components, but because of the modular character of KSimus extensions are easy to develop. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/589400 debian-science-1.0ubuntu1/tasks/neuroscience-modeling0000644000000000000000000001316012025105622017737 0ustar Task: Modeling of neural systems Description: Debian Science packages for modeling of neural systems This metapackage will install Debian packages which might be useful for scientists interested in modeling of real neural systems at different levels (from single neuron to complex networks). . The selection of packages is targeting the application of simulation techniques. Methods developers are referred to the science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging, and med-imaging-dev metapackages for a variety of additional software that might be useful for neuroscience research. ; Added by blends-inject 0.0.2. [now official package] Depends: python-brian Published-Authors: Goodman D.F. and Brette R. Published-DOI: 10.3389/neuro.11.005.2008 Published-In: Front. Neuroinform Published-Title: Brian: a simulator for spiking neural networks in Python Published-Year: 2008 ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: pynn Homepage: http://neuralensemble.org/trac/PyNN Language: Python WNPP: 604159 Responsible: NeuroDebian Team License: CeCILL-2 Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/pynn.git Vcs-Git: git://git.debian.org/git/pkg-exppsy/pynn.git Pkg-URL: http://neuro.debian.net/pkgs/pynn.html Pkg-Description: simulator-independent specification of neuronal network models PyNN allows to code for a model once and run it without modification on any simulator that PyNN supports (currently NEURON, NEST, PCSIM and Brian). PyNN translates standard cell-model names and parameter names into simulator-specific names. ; Added by blends-inject 0.0.5. [Please note here if modified manually] Suggests: moose Homepage: http://moose.sourceforge.net Language: C++, Python License: LGPL Pkg-Description: multiscale simulation environment for neuroscience MOOSE is the Multiscale Object-Oriented Simulation Environment. It is the base and numerical core for large, detailed simulations including Computational Neuroscience and Systems Biology. MOOSE spans the range from single molecules to sub-cellular networks, from single cells to neuronal networks, and to still larger systems. It is backwards-compatible with GENESIS, and forward compatible with Python and XML-based model definition standards like SBML and MorphML. MOOSE is coordinating with the GENESIS-3 project towards the goals of developing educational resources for modeling. ; Added by blends-inject 0.0.5. [Please note here if modified manually] Suggests: pcsim Homepage: http://www.lsm.tugraz.at/pcsim/ Language: C, Python WNPP: 605414 License: GPL-3+ Pkg-Description: simulator of heterogeneous networks of neurons and synapses PCSIM is a tool for simulating heterogeneous networks composed of different model neurons and synapses. This simulator is written in C++ with a primary interface to the programming language Python. It is intended to simulate networks containing up to millions of neurons and on the order of billions of synapses. This is achieved by distributing the network over different nodes of a computing cluster by using MPI. Published-Authors: Pecevski D, Natschläger T and Schuch K Published-DOI: 10.3389/neuro.11.011.2009 Published-In: Front. Neuroinform. 3:11 Published-Title: PCSIM: a parallel simulation environment for neural circuits fully integrated with Python Published-Year: 2009 Remark: last release is more than 1 year ago, but there is development in newbuild branch ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: nest Homepage: http://www.nest-initiative.org/index.php/Software:About_NEST Responsible: Yury V. Zaytsev License: non-FOSS Vcs-Browser: http://git.zaytsev.net/?p=nest-packaging.git;a=summary Vcs-Git: git://git.zaytsev.net/nest-packaging.git Pkg-URL: http://git.zaytsev.net/?p=nest-packaging.git;a=summary Pkg-Description: A simulator for networks of spiking neurons NEST is a simulation system for large networks of biologically realistic point-neurons and neurons with a small number of electrical compartments. Published-Authors: Gewaltig M-O and Diesmann M Published-In: Scholarpedia 2(4):1430 Published-Title: NEST (Neural Simulation Tool) Published-Year: 2007 Registration: http://www.nest-initiative.org/download/Software:Download.php Remark: Mentioned packaging is not providing NEST itself but rather only packaging materials so you could build package yourself. ; Added by blends-inject 0.0.6. [Please note here if modified manually] Suggests: invt Homepage: http://ilab.usc.edu/toolkit/ Language: C++ + Perl, Tcl, Matlab License: GPL-2+ Pkg-Description: iLab Neuromorphic Vision C++ Toolkit The iLab Neuromorphic Vision C++ Toolkit (iNVT, pronounced ``invent'') is a comprehensive set of C++ classes for the development of neuromorphic models of vision. Neuromorphic models are computational neuroscience algorithms whose architecture and function is closely inspired from biological brains. The iLab Neuromorphic Vision C++ Toolkit comprises not only base classes for images, neurons, and brain areas, but also fully-developed models such as our model of bottom-up visual attention and of Bayesian surprise. . Features at a glance: * Low-level neural network simulation classes. * High-level neuromorphic classes. * Neuromorphic models of visual attention. * Hardware interfacing * Parallel processing classes for the simulation of complex models. * Neuromorphic modeling environment. Registration: http://ilab.usc.edu/cgi-bin/yabb/YaBB.pl?board=;action=register ; Added by blends-inject 0.0.7. [now official package - information obtained from package pool] Suggests: xppaut Depends: cnrun debian-science-1.0ubuntu1/tasks/typesetting0000644000000000000000000001057212025105716016050 0ustar Task: typesetting Description: Debian Science typesetting packages This metapackage will install Debian Science packages related to typesetting. You might also be interested in the use::typesetting debtag. Depends: referencer, kbibtex, impose+, pybliographer, texlive-bibtex-extra, \ jabref, bibutils, biber Why: BibTeX and bibliography Depends: feynmf, texlive, texlive-science, texlive-publishers, \ texlive-math-extra, diploma Why: TeX Depends: lyx Why: LyX Depends: texmacs, texmacs-extra-fonts Why: TeXmacs Depends: auctex Why: Emacs editing mode for latex Depends: xfig, transfig Depends: dia Suggests: tellico Suggests: texmaker Suggests: openoffice.org-dmaths Suggests: r-cran-xtable Suggests: csv2latex Depends: bibus Depends: mlpost Depends: latexdiff Depends: libjlatexmath-java Depends: cb2bib Suggests: libgtkmathview-bin Depends: jeuclid-mathviewer Depends: sketch Depends: quaneko Homepage: http://quaneko.sourceforge.net/ WNPP: 324422 License: GPL Responsible: LI Daobing Pkg-Description: An index tool of TXT, PDF, DOC, HTML and others Quaneko is a tool that allows you to quickly search for keywords in the files and directories on the local hard disk. It creates indexes over the words in those files. For you, this means that a typical search query will only take seconds. . quaneko can not only search for words in plain text files but also in various other file formats, depending on its configuration (e.g. Word doc, pdf, html, xml,...) Depends: gpapers Homepage: http://gpapers.org/ License: GPL Pkg-Description: bibliography management software Digital library manager. Think of it as an iTunes for your PDFs. Depends: zotero Homepage: http://www.zotero.org/ License: BSD Pkg-Description: reference manager software Zotero is an easy-to-use yet powerful research tool that helps you gather, organize, and analyze sources (citations, full texts, web pages, images, and other objects), and lets you share the results of your research in a variety of ways. An extension to the popular open-source web browser Firefox, Zotero includes the best parts of older reference manager software (like EndNote)—the ability to store author, title, and publication fields and to export that information as formatted references—and the best parts of modern software and web applications (like iTunes and del.icio.us), such as the ability to interact, tag, and search in advanced ways. Zotero integrates tightly with online resources; it can sense when users are viewing a book, article, or other object on the web, and—on many major research and library sites—find and automatically save the full reference information for the item in the correct fields. Since it lives in the web browser, it can effortlessly transmit information to, and receive information from, other web services and applications; since it runs on one’s personal computer, it can also communicate with software running there (such as Microsoft Word). And it can be used offline as well (e.g., on a plane, in an archive without WiFi). . * Automatic capture of citation information from web pages * Storage of PDFs, files, images, links, and whole web pages * Flexible notetaking with autosave * Fast, as-you-type search through your materials * Playlist-like library organization, including saved searches (smart collections) and tags * Platform for new forms of digital research that can be extended with other web tools and services * Formatted citation export (over 1100 styles and growing) * Integration with Microsoft Word and OpenOffice * Saves records and notes in several languages * Integration with WordPress and other blogging software * Remote library backup * Advanced search and data mining tools * Wide variety of import/export Suggests: pymarc WNPP: 585583 Homepage: http://github.com/edsu/pymarc License: BSD Responsible: Edward Betts Pkg-URL: http://edwardbetts.com/debian Pkg-Description: read, write and modify MARC bibliographic data pymarc is a Python library for working with MARC21 bibliographic data loosely based on the MARC/Perl suite of modules (http://marcpm.sf.net). debian-science-1.0ubuntu1/tasks/meteorology0000644000000000000000000001050012132726633016033 0ustar Task: Meteorology Description: Debian Science Meteorology packages This metapackage is part of the Debian Pure Blend "Debian Science" and installs packages related to Meteorology and Climate. Depends: cdo Why: Widely-used File format manipulation utility Depends: nco Depends: dballe Depends: zygrib Why: Used as default tool for viewing GRIB files. Depends: ncview Depends: grads Why: Used as default tool for viewing BUFR files. Depends: ferret-vis Pkg-Description: Analysis and Visualisation tool for meteorologists Depends: magics++ Depends: freefoam Depends: visit Homepage: http://www.llnl.gov/visit/ WNPP: 395573 Responsible: Alastair McKinstry Pkg-Description: Interactive parallel visualization and graphical analysis tool Why: Used for 3-D visualisation of netCDF datasets. Suggests: paraview Why: 3-D visualisation of climate (netCDF) files Depends: libgrib-api-tools Responsible: Enrico Zini Depends: hdf-eos4 Pkg-Description: Extension to HDF4 to support Earth Observing System datatypes HDF-EOS is a software library that is an extension of National Center for Supercomputing Applications (NCSA) HDF. The library supports the construction of new data structures: Grid, Point and Swath. Depends: hdf-eos5 Pkg-Description: Extension to HDF5 to support Earth Observing System datatypes HDF-EOS is a software library that is an extension of National Center for Supercomputing Applications (NCSA) HDF. The library supports the construction of new data structures: Grid, Point and Swath. Depends: ecaccess Depends: geonetwork Homepage: http://geonetwork-opensource.org Responsible: Alastair McKinstry WNPP: 529453 License: GPL Pkg-Description: Catalog application to manage spatially referenced resources through the web Network opensource is a standards based, Free and Open Source catalog application to manage spatially referenced resources through the web. It provides powerful metadata editing and search functions as well as an embedded interactive web map viewer. This website contains information related to the use of the software. Depends: ncl WNPP: 531982 License: BSD Homepage: http://www.ncl.ucar.edu/overview.shtml Pkg-Description: NCAR Command Language and NCAR Graphics package The NCAR Command Language (NCL) is a free interpreted language designed specifically for scientific data processing and visualization. NCL has robust file input and output. It can read and write netCDF-3, netCDF-4 classic (as of version 4.3.1), HDF4, binary, and ASCII data, and read HDF-EOS2, GRIB1 and GRIB2 (as of version 4.3.0). The graphics are world class and highly customizable. Depends: python-netcdf4 Depends: python-grib License: BSD Homepage: https://pygrib.googlecode.com/svn/trunk/docs/index.html Responsible: Alastair McKinstry Pkg-Description: python library for reading/writing GRIB files Python module for reading and writing GRIB (editions 1 and 2) files. GRIB is the World Meterological Organization standard for distributing gridded data. The module is a python interface to the GRIB API C library from the European Centre for Medium-Range Weather Forecasts (ECMWF). Depends: python-drslib Depends: python-cmor Depends: python-spherepack Pkg-Description: Python interface to the spherepack scientific library. This is a python interface to spherepack, a library for calculations on spheres (geophysical). Depends: cmip5-cmor-tables Suggests: gnudatalanguage, r-base Why: Used for data manipiulation Suggests: octave-octcdf Why: Used for data manipiulation Suggests: gerris Suggests: python-openturns Why: Uncertainty quantification in numerical simulation Depends: aweather Depends: libdap-bin, libdap-doc Suggests: pydap WNPP: 640037 License: MIT Responsible: Sandro Tosi Pkg-Description: DAP (Data Access Protocol) client and server This is a Python implementation of the Data Access Protocol, a scientific protocol for data access developed by the OPeNDAP team (http://opendap.org). This implementation is developed from scratch, following the latest specification of the protocol (DAP 2.0 Draft Community Standard 2005/04/27) and based on my experience with OPeNDAP servers on the wild. Depends: vistrails Why: Used by CDAT, vistrails is a workflow tool used to track changes made when investigating climate data. debian-science-1.0ubuntu1/tasks/dataacquisition0000644000000000000000000001165611772115066016666 0ustar Task: Data acquisition Description: Debian Science data acquisition packages This metapackage will install Debian Science packages related to data acquisition. This might be used in several sciences (as for instance science-viewing and science-typesetting). Depends: engauge-digitizer Suggests: gnudatalanguage Depends: qtdmm Depends: g3data Suggests: libgpib-bin Depends: ktimetrace Depends: netcdf-bin Suggests: comedi-source Suggests: rtai Suggests: xenomai-runtime Depends: python-sardana Suggests: linux-image-2.6-rt Responsible: kernel@pengutronix.de Homepage: http://www.pengutronix.de/software/linux-rt/debian_en.html License: GPL Pkg-URL: http://debian.pengutronix.de Pkg-Description: Stock Linux kernel with RT-Preempt patch The RT-Preempt (http://rt.wiki.kernel.org) project provides patches to make Linux kernel capable of fulfilling hard realtime requirements. The aim is to eliminate all preemptivity and reactivity problems in the kernel over the time by adding deterministic preemption points. The -rt patches are constantly being worked on for mainline by the community. . Pengutronix's Realtime Linux for Debian project provides builds of the stock Linux kernel with the RT-Preempt patch (but without Debian patches). Remark: The upstream kernel sources are not considered DFSG-free, so the packages are available from the non-free area only. Suggests: rt-tests Suggests: gpsd Depends: jaaa Depends: ghkl Depends: narval-utils Depends: python-visa Homepage: http://pyvisa.sourceforge.net/ License: MIT Pkg-Description: control measurement devices and test equipment via GPIB, RS232, or USB A Python package with bindings to the "Virtual Instrument Softwares Architecture" VISA library, in order to control measurement devices and test equipment via GPIB, RS232, or USB. . Articles about pyvisa: * G. Varoquaux has written an interesting article describing the use of python and pyvisa for experimental control. Agile computer control of a complex experiment. Computing in Science and Engineering 10(2), 55 (2008). * Writing a graphical application for scientific programming using TraitsUI Suggests: tango-db, tango-starter, tango-accesscontrol, python-pytango, python-taurus Depends: mx-dataacquisition Homepage: http://mx.iit.edu/ License: MIT Pkg-URL: http://debian-xray.iit.edu/pool/main/m/mx1.4/ Responsible: Carlo Segre Pkg-Description: data acquisition and control system MX is a data acquisition and control system that is designed to serve several functions: * As a portable toolkit for writing data acquisition and control programs. * As a standalone system capable of controlling entire experiments. * As a platform for building device control servers to be used by other applications. * As a way of extending other control systems and of glueing disparate control systems together. Depends: epics Homepage: http://www.aps.anl.gov/epics/ License: EPICS base license (BSD like) Pkg-URL: http://debian-xray.iit.edu/pool/main/e/epics/ Responsible: Carlo Segre Pkg-Description: Experimental Physics and Industrial Control System EPICS is a set of Open Source software tools, libraries and applications developed collaboratively and used worldwide to create distributed soft real-time control systems for scientific instruments such as a particle accelerators, telescopes and other large scientific experiments. Depends: plot-digitizer Homepage: http://plotdigitizer.sourceforge.net/ License: GPL Responsible: Stuart Prescott Pkg-Description: digitize scanned plots of functional data An easy to use Java program that allows you to digitize data points off of scanned plots, scaled drawings, or orthographic photographs. Includes an automatic digitization feature that can automatically digitize many types of functional data. ; Added by blends-inject 0.0.6. [Please note here if modified manually] Suggests: hart Homepage: http://hart.sourceforge.net/ Language: C License: GPL Pkg-Description: toolbox to generate DAQ Scicos-blocks for hardware The HART (Hardware Access in Real-Time) Toolbox can be used to generate Scicos-blocks for hardware that have a C/C++ interface. The blocks can be used under Linux for soft and hard real time tasks (RTAI). Blocks are provided for DAQ (COMEDI) ; Added by blends-inject 0.0.6. [Now official package] Depends: libfreenect-dev Depends: opendap WNPP: 641315 Responsible: Mathieu Malaterre Homepage: http://www.opendap.org License: LGPL Language: Java Pkg-Description: Java Network Data Access Protocol OPeNDAP is a framework that simplifies all aspects of scientific data networking. . OPeNDAP provides software which makes local data accessible to remote locations regardless of local storage format. . OPeNDAP also provides tools for transforming existing applications into OPeNDAP clients (i.e., enabling them to remotely access OPeNDAP served data). debian-science-1.0ubuntu1/tasks/linguistics0000644000000000000000000000425212131273227016025 0ustar Task: Linguistics Description: Debian Science Linguistics packages This metapackage is part of the Debian Pure Blend "Debian Science" and installs packages related to Linguistics. Depends: wordnet Depends: apertium, link-grammar Depends: artha Depends: timbl, timblserver, mbt, mbtserver, ucto, dimbl, frog Homepage: http://ilk.uvt.nl/ Why: Software (co)developed and used by Tilburg Universities' ILK research group, in cooperation with the Language Technology Research group of CLiPS of the University of Antwerp, Belgium. ILK develops and employs inductive learning algorithms in solving natural language problems, useful in the areas of Language Engineering as well as Linguistic and Cognitive Modelling. Suggests: libtimbl3-dev, libtimblserver2-dev, libmbt0-dev, libucto1-dev, libfolia1-dev Homepage: http://ilk.uvt.nl/ Why: Software (co)developed and used by Tilburg Universities' ILK research group, in cooperation with the Language Technology Research group of CLiPS, Antwerp. These packages are useful for software developers when developing or extending ILK's Natural Language Processing tools. Suggests: python-timbl Suggests: wnsqlbuilder Homepage: http://wnsqlbuilder.sf.net License: GPL Pkg-Description: SQL version of WordNet 3.0 WordNet SQL Builder is a Java utility to generate SQL database from WordNet standard database as released by the WordNet Project (Princeton University) . Features * Support for MySql and PostGreSQL. * Complete port (however, orphaned morphological forms are dropped, and so are VerbNet/XWordNet data that cannot be linked to WordNet entries). * Incremental build support. * Retains synset index as primary key allowing easy reference to wordnet original database * Includes support for WordNet 3.0 * Includes support for WordNet 2.0 to 2.1, 2.1 to 3.0, 2.0 to 3.0 sense maps * Includes support for VerbNet 2.3 * Includes support for XWordNet 2.0-1.1 * Ready-to-use database (see wnsqldatabase package in download section) including - WordNet 3.0 - WordNet 2.0 to 2.1, 2.1 to 3.0, 2.0 to 3.0 sense maps - VerbNet 2.3 - XWordNet 2.0-1.1 - British National Corpus statistical data (for commonly used-words) debian-science-1.0ubuntu1/tasks/neuroscience-datasets0000644000000000000000000003631311723522074017766 0ustar Task: Neuroscience Datasets Description: Debian Science packages for Neuroscience Datasets This metapackage will install Debian packages that provide neuroscientific datasets. These datasets can be useful as common data files for applications (e.g. stereotaxic atlases), as example data for online tutorials or teaching, and as input data for analysis algorithms in demonstrations or test suites. Depends: mni-icbm152-nlin-2009 Homepage: http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 License: custom, DFSG-compliant Responsible: NeuroDebian team Pkg-URL: http://neuro.debian.net/pkgs/mni-icbm152-nlin-2009a.html Pkg-Description: MNI stereotaxic space human brain template This is an unbiased standard magnetic resonance imaging template volume for the normal human population. It has been created by the Montreal Neurological Institute (MNI) using anatomical data from the International Consortium for Brain Mapping (ICBM). . The package provides a 1x1x1 mm and 0.5x0.5x0.5 mm resolution templates (hemissphere-symetric and asymetric non-linearily co-registered versions), some including T1w, T2w, PDw modalities, T2 relaxometry, and tissue probability maps. In addition, it contains a lobe atlas, and masks for brain, eyes and face. Published-Authors: V.S. Fonov, A.C. Evans, R.C. McKinstry, C.R. Almli and D.L. Collins Published-Title: Unbiased nonlinear average age-appropriate brain templates from birth to adulthood. Published-In: NeuroImage, 47, Supplement 1: 102 Published-Year: 2009 Remark: This package is waiting for the Debian data package archive to become available. Depends: mni-colin27-nifti Homepage: http://packages.bic.mni.mcgill.ca/tgz/ License: custom, DFSG-compliant Responsible: NeuroDebian team Pkg-URL: http://neuro.debian.net/pkgs/mni-colin27-nifti.html Pkg-Description: Talairach stereotaxic space template This template MRI volume was created from 27 T1-weighted MRI scans of a single individual that have been transformed into the Talairach stereotaxic space. The anatomical image is complemented by a brain and a head mask. All images are in 1x1x1 mm resolution. . This package provides the template in NIfTI format. Published-Authors: C.J. Holmes, R. Hoge, L. Collins, R. Woods, A.W. Toga, A.C. Evans Published-Title: Enhancement of MR images using registration for signal averaging. Published-In: J Comput Assist Tomogr, 22: 324-333 Published-Year: 1998 Remark: This package is waiting for the Debian data package archive to become available. Depends: haxby2001-faceobject Homepage: http://data.pymvpa.org/datasets/haxby2001 License: CC-BY-SA Responsible: NeuroDebian team Pkg-URL: http://neuro.debian.net/pkgs/haxby2001-faceobject.html Pkg-Description: face and object processing in ventral temporal cortex (fMRI) This is data from a block-design fMRI study on face and object representation in human ventral temporal cortex. The full datasets consists of 6 subjects with 12 runs per subject. In each run, the subjects passively viewed grey scale images of eight object categories, grouped in 24s blocks separated by rest periods. Each image was shown for 500ms and was followed by a 1500ms inter-stimulus interval. Full-brain fMRI data were recorded with a volume repetition time of 2.5s. Published-Authors: James V. Haxby, M. I. Gobbini, M. L. Furey, A. Ishai, J. L. Schouten, P. Pietrini Published-Title: Distributed and overlapping representations of faces and objects in ventral temporal cortex. Published-In: Science, 293: 2425-2430 Published-Year: 2001 Published-DOI: 10.1126/science.1063736 Remark: This package is waiting for the Debian data package archive to become available. Depends: fsl-harvard-oxford-atlases License: custom, non-commerical Responsible: NeuroDebian team Remark: This package is waiting for the Debian data package archive to become available. Pkg-URL: http://neuro.debian.net/pkgs/fsl-harvard-oxford-atlases.html Pkg-Description: probabilistic atlas of human cortical and subcortical brain areas Probabilistic atlases covering 48 cortical and 21 subcortical structural areas, derived from structural data and segmentations kindly provided by the Harvard Center for Morphometric Analysis. . T1-weighted images of 21 healthy male and 16 healthy female subjects (ages 18-50) were individually segmented using semi-automated tools developed in-house. The T1-weighted images were affine-registered to MNI152 space using FLIRT (FSL), and the transforms then applied to the individual labels. Finally, these were combined across subjects to form population probability maps for each label. . This package is part of FSL. Published-Authors: Rahul S Desikan and Florent Segonne and Bruce Fischl and Brian T Quinn and Bradford C Dickerson and Deborah Blacker and Randy L Buckner and Anders M Dale and R Paul Maguire and Bradley T Hyman and Marilyn S Albert and Ronald J Killiany Published-Title: An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. Published-In: Neuroimage, 31: 968–980 Published-Year: 2006 Published-DOI: 10.1016/j.neuroimage.2006.01.021 Depends: fsl-juelich-histological-atlas License: custom, non-commerical Responsible: NeuroDebian team Remark: This package is waiting for the Debian data package archive to become available. Pkg-URL: http://neuro.debian.net/pkgs/fsl-juelich-histological-atlas.html Pkg-Description: brain atlas based on cyto- and myelo-architectonic segmentations A probabilistic atlas created by averaging multi-subject post-mortem cyto- and myelo-architectonic segmentations, performed by the team of Profs Zilles and Amunts at the Research Center Jülich and kindly provided by Simon Eickhoff. . The atlas contains 32 grey matter structures and 10 white matter structures. This is the same data as used in Eickhoff's Anatomy Toolbox v1.5. The atlas is based on the microscopic and quantitative histological examination of ten human post-mortem brains. The histological volumes of these brains were 3D reconstructed and spatially normalised into the space of the MNI single subject template to create a probabilistic map of each area. For the FSL version of this atlas, these probabilistic maps were then linearly transformed into MNI152 space. . This package is part of FSL. Published-Authors: Simon B Eickhoff, Klaas E Stephan, Hartmut Mohlberg, Christian Grefkes, Gereon R Fink, Katrin Amunts, Karl Zilles Published-Title: A new SPM toolbox for combining probabilistic cytoarchitectonic maps and functional imaging data. Published-In: Neuroimage, 25: 1325–1335 Published-Year: 2005 Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/15850749 Depends: fsl-jhu-dti-whitematter-atlas License: custom, non-commerical Responsible: NeuroDebian team Remark: This package is waiting for the Debian data package archive to become available. Pkg-URL: http://neuro.debian.net/pkgs/fsl-jhu-dti-whitematter-atlas.html Pkg-Description: human brain white-matter atlas There are two white-matter atlases, both kindly provided by Dr. Susumu Mori, Laboratory of Brain Anatomical MRI, Johns Hopkins University. . In the ICBM-DTI-81 white-matter labels atlas, 50 white matter tract labels were created by hand segmentation of a standard-space average of diffusion MRI tensor maps from 81 subjects; mean age 39 (18:59), M:42, F: 39. The diffusion data was kindly provided by the ICBM DTI workgroup. . In the JHU white-matter tractography atlas, 20 structures were identified probabilistically by averaging the results of running deterministic tractography on 28 normal subjects (mean age 29, M:17, F:11). . This package is part of FSL. Published-Authors: Kegang Hua, Jiangyang Zhang, Setsu Wakana, Hangyi Jiang, Xin Li, Daniel S Reich, Peter A Calabresi, James J Pekar, Peter C M van Zijl, Susumu Mori Published-Title: Tract probability maps in stereotaxic spaces: analyses of white matter anatomy and tract-specific quantification. Published-In: Neuroimage, 39: 336–347 Published-Year: 2008 Published-DOI: 10.1016/j.neuroimage.2007.07.053 Depends: fsl-mni-structural-atlas License: custom, non-commerical Responsible: NeuroDebian team Remark: This package is waiting for the Debian data package archive to become available. Pkg-URL: http://neuro.debian.net/pkgs/fsl-mni-structural-atlas.html Pkg-Description: hand-segmented single-subject human brain atlas 9 anatomical structural regions, kindly provided by Jack Lancaster at the Research Imaging Center, UTHSCSA, Texas (originally from the McConnell Brain Imaging Centre, MNI). . A single subject's structural image was hand segmented, and the labels were then propagated to more than 50 subjects' structural images using nonlinear registration. Each resulting labelled brain was then transformed into MNI152 space using affine registration, before averaging segmentations across subjects to produce the final probability images. . This package is part of FSL. Published-Authors: J. Mazziotta, A. Toga, A. Evans, P. Fox, J. Lancaster, K. Zilles, R. Woods, T. Paus, G. Simpson, B. Pike and others Published-Title: A probabilistic atlas and reference system for the human brain: International Consortium for Brain Mapping (ICBM) Published-In: The Royal Society Philosophical Transactions B, 356: 1293–1322 Published-Year: 2001 Depends: fsl-talairach-daemon-atlas License: custom, non-commerical Responsible: NeuroDebian team Remark: This package is waiting for the Debian data package archive to become available. Pkg-URL: http://neuro.debian.net/pkgs/fsl-talairach-daemon-atlas.html Pkg-Description: structural anatomy labels of the Talairach atlas A conversion of the original Talairach structural labellings, kindly provided by Jack Lancaster and Diana Tordesillas Gutiérrez at the Research Imaging Center, UTHSCSA, Texas. . This is a digitised version of the original (coarsely sliced) Talairach atlas (Lancaster 2000) after the application of a correcting affine transform (Lancaster 2007) to register it into MNI152 space. . This package is part of FSL. Published-Authors: J L Lancaster, M G Woldorff, L M Parsons, M Liotti, C S Freitas, L Rainey, P V Kochunov, D Nickerson, S A Mikiten, P T Fox Published-Title: Automated Talairach atlas labels for functional brain mapping. Published-In: Human Brain Mapping, 10: 120–131 Published-Year: 2000 Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10912591 Depends: fsl-oxford-thalamic-connectivity-atlas License: custom, non-commerical Responsible: NeuroDebian team Remark: This package is waiting for the Debian data package archive to become available. Pkg-URL: http://neuro.debian.net/pkgs/fsl-oxford-thalamic-connectivity-atlas.html Pkg-Description: probabilistic brain atlas of thalamic white-matter connectivity A probabilistic atlas of 7 sub-thalamic regions, segmented according to their white-matter connectivity to cortical areas, kindly provided by Heidi Johansen-Berg and Timothy Behrens, FMRIB. . This connectivity atlas reports probability of anatomical connection from points in the thalamus to each of 7 cortical zones. These probabilities are calculated using probabilistic diffusion tractography in multiple subjects. . This package is part of FSL. Published-Authors: TEJ Behrens, H. Johansen-Berg, MW Woolrich, SM Smith, CAM Wheeler-Kingshott, PA Boulby, GJ Barker, EL Sillery, K. Sheehan, O. Ciccarelli and others Published-Title: Non-invasive mapping of connections between human thalamus and cortex using diffusion imaging. Published-In: Nature Neuroscience, 6: 750–757 Published-Year: 2003 Depends: fsl-bangor-cerebellar-atlas License: custom, non-commerical Responsible: NeuroDebian team Remark: This package is waiting for the Debian data package archive to become available. Pkg-URL: http://neuro.debian.net/pkgs/fsl-bangor-cerebellar-atlas.html Pkg-Description: probabilistic atlas of the human cerebellum This is a probabilistic atlas of the cerebellar lobules in the anatomical space defined by the MNI152 template. Lobules were masked separately on T1-weighted MRI scans (1 mm isotropic resolution) of 20 healthy young participants (10 male, 10 female, average age 23.7 yrs). These cerebella were then aligned to the standard or non-linear version of the whole-brain MNI152 template using a number of commonly used normalization algorithms, or to a previously published cerebellum-only template (Diedrichsen, J., 2006. A spatially unbiased atlas template of the human cerebellum. NeuroImage 33, 127-138). . This package is part of FSL. Published-Authors: Jörn Diedrichsen, Joshua H Balsters, Jonathan Flavell, Emma Cussans, Narender Ramnani Published-Title: A probabilistic MR atlas of the human cerebellum. Published-In: Neuroimage, 46: 39–46 Published-Year: 2009 Published-DOI: 10.1016/j.neuroimage.2009.01.045 Depends: mclaren-rhesus-macaque-atlas License: GPL-3 Homepage: http://brainmap.wisc.edu/pages/2-Rhesus-Macaque-Atlases-for-functional-and Pkg-URL: http://neuro.debian.net/debian/pool/main/m/mclaren-rhesus-macaque-atlas/ Responsible: NeuroDebian team Remark: Upstream agreed to change the license to GPL-3 (might not yet be reflected on the webpage yet) Pkg-Description: MRI-based brain atlas of the rhesus macaque monkey A population-average MRI-based atlas collection for the rhesus macaque (Macaca mulatta) that can be used with common brain mapping packages such as SPM or FSL. In addition to T1-weighted atlas data, probabilistic tissue classification maps and T2-weighted atlases were also created. Theses atlases are aligned to the MRI volume from the Saleem, K.S. and Logothetis, N.K. (2006) atlas providing an explicit link to histological sections. Additionally, there is a transform to integrate these atlases with the F99 surface-based atlas in CARET. Published-Authors: McLaren DG, Kostmatka KJ, Oakes TR, Kroenke CD, Kohama SG, Matochik JA, Ingram DK, and Johnson SC. Published-Title: A Population-Average MRI-Based Atlas Collection of the Rhesus Macaque. Published-In: Neuroimage, 45: 52-9 Published-Year: 2009 Published-DOI: 10.1016/j.neuroimage.2008.10.058 Depends: sri24-atlas License: CC-BY-SA-3.0 Responsible: NeuroDebian team Homepage: http://www.nitrc.org/projects/sri24 Pkg-URL: http://neuro.debian.net/pkgs/sri24-atlas.html Pkg-Description: MRI-based brain atlas of normal adult human brain anatomy SRI24 is an MRI-based atlas of normal adult human brain anatomy, generated by template-free nonrigid registration from images of 24 normal control subjects. . The atlas comprises T1, T2, and PD weighted structural MRI, tissue probability maps (GM, WM, CSF), maximum-likelihood tissue segmentation, DTI-based measures (FA, MD, longitudinal and transversal diffusivity), and two labels maps of cortical regions and subcortical structures. The atlas is provided at 1mm isotropic image resolution in NIfTI format. Published-Authors: Torsten Rohlfing, Natalie M. Zahr, Edith V. Sullivan. Adolf Pfefferbaum Published-Title: The SRI24 multichannel atlas of normal adult human brain structure Published-In: Human Brain Mapping, vol. 31, no. 5 Published-Year: 2010 Published-DOI: 10.1002/hbm.20906 Remark: This package is waiting for the Debian data package archive to become available. debian-science-1.0ubuntu1/tasks/robotics0000644000000000000000000001301111754134544015315 0ustar Task: Robotics Description: Debian Robotics packages This metapackage is part of the Debian Pure Blend "Debian Science" and installs packages related to Robotics. . You might also be interested in the science-engineering metapackage. Depends: rtai, xenomai-runtime Depends: libcv-dev Depends: libcomedi0 Comment: Debian version is quite old - needs update Depends: octave, gnuplot Depends: libcoin60-runtime, libvtk5.4, libboost-dev Depends: libopenigtlink1 Depends: libode-dev Depends: morse-simulator WNPP: 670577 Depends: solid WNPP: 500616 Homepage: http://www.dtecta.com License: GPL, QPL Language: C++ Pkg-Description: Software library for collision detection of geometric objects in 3D space. Collision detection is the process of detecting pairs of objects that are intersecting or are within a given proximity of each other. SOLID contains operations for performing intersection tests and proximity queries on a wide variety of shape types, including: deformable triangle meshes, boxes, ellipsoids, and convex polyhedra. . Since it exploits temporal coherence in a number of ways, SOLID is especially useful for detecting collisions between objects that move smoothly over time. The motions of objects are controlled by the client application, and are not determined or affected by SOLID. . Although it can be used for physics-based simulations, SOLID is not a physics engine by itself. SOLID leaves it up to the application programmer how the laws of physics are implemented. Depends: robot-player Depends: d-collide Homepage: http://d-collide.ematia.de/ License: BSD Responsible: Leopold Palomo-Avellaneda Pkg-Description: D-Collide is a real-time collision detection library aimed at performance and accuracy, that supports rigid objects as well as deformables - such as cloth - including self-collision detection. Depends: rtnet Homepage: http://www.rtnet.org License: GPL Responsible: Leopold Palomo-Avellaneda Pkg-Description: hard real-time network protocol stack RTnet is an Open Soure hard real-time network protocol stack for Xenomai and RTAI (real-time Linux extensions). It makes use of standard Ethernet hardware and supports several popular NIC chip sets, including Gigabit Ethernet. Moreover, Ethernet-over-1394 support is available based on the RT-FireWire protocol stack. Depends: orca Homepage: http://orca-robotics.sourceforge.net/orca/index.html License: LGPL and GPL Responsible: Leopold Palomo-Avellaneda Pkg-Description: developing component-based robotic systems Orca is an open-source framework for developing component-based robotic systems. It provides the means for defining and developing the building-blocks which can be pieced together to form arbitrarily complex robotic systems, from single vehicles to distributed sensor networks. Depends: roboop Homepage: http://www.cours.polymtl.ca/roboop/ License: GPL Responsible: Leopold Palomo-Avellaneda Pkg-Description: synthesis, and simulation of robotic manipulator models ROBOOP is a C++ robotics object oriented programming toolbox suitable for synthesis, and simulation of robotic manipulator models in an environment that provides ``MATLAB like'' features for the treatment of matrices. Its is a portable tool that does not require the use of commercial software. Depends: orocos-rtt Homepage: http://www.orocos.org/rtt License: GPL + runtime exception Responsible: Leopold Palomo-Avellaneda Pkg-URL: http://svn.fmtc.be/debian Pkg-Description: Orocos Real-Time Toolkit The Orocos Real-Time Toolkit (RTT) is not an application in itself, but it provides the infrastructure and the functionalities to build robotics applications in C++. The emphasis is on real-time, online interactive and component based applications. Depends: orocos-kdl Homepage: http://www.orocos.org/kdl License: LGPL Responsible: Leopold Palomo-Avellaneda Pkg-Description: Kinematics and Dynamics Library The Kinematics and Dynamics Library (KDL) develops an application independent framework for modelling and computation of kinematic chains, such as robots, biomechanical human models, computer-animated figures, machine tools, etc. It provides class libraries for geometrical objects (point, frame, line,... ), kinematic chains of various families (serial, humanoid, parallel, mobile,... ), and their motion specification and interpolation. Depends: orocos-ocl Homepage: http://www.orocos.org/ocl License: LGPL Responsible: Leopold Palomo-Avellaneda Pkg-URL: http://svn.fmtc.be/debian Pkg-Description: Orocos Component Library The Orocos Component Library uses the Real-Time Toolkit (RTT) for constructing all its components. Some components use the Kinematics and Dynamics Library (KDL), the Bayesian Filtering Library (BFL) or other libraries. Depends: orocos-bfl Homepage: http://www.orocos.org/bfl License: GPL + runtime exception Responsible: Leopold Palomo-Avellaneda Pkg-URL: http://people.mech.kuleuven.be/~tdelaet/bfl Pkg-Description: framework for inference in Dynamic Bayesian Networks The Bayesian Filtering Library (BFL) provides an application independent framework for inference in Dynamic Bayesian Networks, i.e., recursive information processing and estimation algorithms based on Bayes' rule, such as (Extended) Kalman Filters, Particle Filters (or Sequential Monte Carlo methods), etc. These algorithms can, for example, be run on top of the Realtime Services, or be used for estimation in Kinematics & Dynamics applications. debian-science-1.0ubuntu1/tasks/machine-learning0000644000000000000000000001320012121070204016647 0ustar Task: Machine Learning Description: Debian Science Machine Learning packages This metapackage will install Debian packages which might be useful for scientists interested in machine learning. Included packages range from knowledge-based (expert) inference systems to software implementing dominant nowadays statistical methods. Depends: python-pyke, gprolog, yap Comment: Prolog (and alike) systems for inductive reasoning Depends: libtorch3-dev Depends: libshogun-dev, libfann-dev, libsvm-dev, libcomplearn-dev, \ libqsearch-dev, liblinear-dev, libocas-dev Comment: above libraries have also variety of interfaces to high-level scripting languages (e.g. Python) and even possibly some interactive GUI Depends: python-scikits-learn, python-mdp, python-mlpy Comment: Native Python toolkits Depends: weka Depends: vowpal-wabbit Depends: r-cran-mass, r-cran-bayesm, r-cran-class, r-cran-cluster, \ r-cran-msm, r-cran-mcmcpack, r-cran-mnp, r-cran-amore Comment: R packages Depends: python-mvpa Why: Framework for statistical learning analysis of large datasets. Published-Title: PyMVPA: a unifying approach to the analysis of neuroscientific data Published-Authors: Michael Hanke, Yaroslav O. Halchenko, Per B. Sederberg, Emanuele Olivetti, Ingo Fründ, Jochem W. Rieger, Christoph S. Herrmann, James V. Haxby, Stephen José Hanson, Stefan Pollmann Published-In: Frontiers in Neuroinformatics, 3:3 Published-Year: 2009 Published-URL: http://www.frontiersin.org/neuroinformatics/paper/10.3389/neuro.11/003.2009/ Published-DOI: 10.3389/neuro.11.003.2009 Depends: python-statsmodels Why: Statistical models Depends: root-system Depends: libroot-tmva-dev, libroot-montecarlo-vmc-dev, libroot-math-mlp-dev X-Comment: Somebody injected the libraries from the ROOT system explicitely here for machine-learning - so these were included since root-system is packaged again Depends: autoclass, mcl Comment: Applications Depends: scilab-ann Depends: libga-dev, libevocosm-dev, pgapack, python-genetic, octave-ga, \ python-pyevolve Comment: Evolutionary algorithm libraries in various languages Depends: flann Homepage: http://www.cs.ubc.ca/~mariusm/index.php/FLANN/FLANN Language: C++ WNPP: 581903 License: BSD Pkg-Description: Fast Library for Approximate Nearest Neighbors FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces. It contains a collection of algorithms we found to work best for nearest neighbor search and a system for automatically choosing the best algorithm and optimum parameters depending on the dataset. Depends: lua-torch5 Homepage: http://torch5.sourceforge.net Language: C, Lua WNPP: 490204 License: BSD Pkg-Description: A matlab-like environment for state-of-the-art machine learning algorithms. Torch5 provides a Matlab-like environment for state-of-the-art machine learning algorithms. It is easy to use and provides a very efficient implementation, thanks to an easy and fast scripting language (Lua) and a underlying C implementation. ; Added by blends-inject 0.0.6. [Please note here if modified manually] Depends: lush Why: LUSH is a generic Lisp environment for numeric computation, but because ML is of primary interest of the authors, thus lush contains quite a few ML libraries (ANN, SVM, etc). Published-Authors: Leon Bottou and Yann LeCun Published-Title: The Lush manual Published-URL: http://lush.sf.net Published-Year: 2002 Depends: libcv-dev, python-opencv Why: OpenCV provides a set of ML methods for pattern recognition within the context of computer vision Depends: libvigraimpex-dev, python-vigra Why: VIGRA is a computer vision library that provides customizable algorithms and datastructures, allowing for easy adaptation in applications. Depends: pybrain Homepage: http://www.pybrain.org Language: Python WNPP: 587069 License: BSD Pkg-Description: Modular Machine Learning Library PyBrain is a modular machine learning library for Python. Its goal is to offer flexible, easy-to-use yet still powerful algorithms for Machine Learning Tasks and a variety of predefined environments to test and compare your algorithms. . PyBrain currently features algorithms for Supervised Learning, Unsupervised Learning, Reinforcment Learning and Black-box Optimization. Depends: libshark-dev Homepage: http://shark-project.sourceforge.net Language: C++ WNPP: 595485 License: GPL-2+ Pkg-Description: Library for Designing and Optimizing Adaptive Systems SHARK is a modular C++ library for the design and optimization of adaptive systems. It provides methods for linear and nonlinear optimization, in particular evolutionary and gradient-based algorithms, kernel-based learning algorithms and neural networks, and various other machine learning techniques. SHARK serves as a toolbox to support real world applications as well as research in different domains of computational intelligence and machine learning. Suggests: science-statistics, science-numericalcomputation Suggests: libacovea-dev Suggests: science-typesetting Meta-Suggests: svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/typesetting ; Added by blends-inject 0.0.7. [now official package] Depends: python-pebl Depends: python-orange License: GPLv3 Homepage: http://orange.biolab.si/ Pkg-URL: http://orange.biolab.si/debian/ Responsible: Mitar Pkg-Description: Data mining framework Orange is a component-based data mining software. It includes a range of data visualization, exploration, preprocessing and modeling techniques. It can be used through a nice and intuitive user interface or, for more advanced users, as a module for Python programming language. Depends: python-pymcdebian-science-1.0ubuntu1/tasks/engineering-dev0000644000000000000000000000330012264700327016532 0ustar Task: Engineering-dev Description: Debian Science Engineering-dev packages This metapackage will install Debian Science packages which might be helpful for development of applications for Engineering. . You might also be interested in the science-engineering metapackage. Depends: libalberta2-dev Depends: libfvm-dev Depends: libcgns-dev Depends: libitpp-dev Depends: freefoam-dev Depends: libexodusii-dev Depends: libadios-dev, libbox-dev, libsilo-dev, libxdmf-dev Why: I/O format libraries used by various codes. Write in these formats for visualizartion systems such as VisIt, Paraview to work. Suggests: libgtkdatabox-0.9.1-1-dev Comment: We have to find a way to make sure that version number changes in the library will be regarded effectively in the metapackages. Suggests: libgtkdataboxmm-dev Depends: libgetfem++-dev Depends: libhdf5-serial-dev, libjhdf5-java, libjhdf4-java Depends: pycgns Homepage: http://elsa.onera.fr/CGNS/releases/ License: GPL-2 Pkg-Description: Package is a Python binding to the CGNS library The package contains a wrapper on top of the ADF and MLL APIs, some tools, demos, tests, and examples taken from the CGNS tutorial.. Suggests: libqwt-dev | libqwt5-qt4-dev Depends: libopencascade-dev Depends: liblife-dev Why: Partial differential equations library, FEA, CFD Depends: libluminate-dev Depends: libopenturns-dev Depends: libmadlib-dev Why: Mesh adaptation Depends: libslepc3.0.0-dev Why: Generalized and standard eigenvalue solver framework, applications to modal analysis Depends: libelmer-dev Depends: libmed-dev, libmedc-dev, libmedimport-dev Depends: libnetcdf-dev, python-netcdf Depends: libnetcdf-java Depends: syfi-dev Depends: libmesh-dev debian-science-1.0ubuntu1/tasks/statistics0000644000000000000000000001137012264700327015664 0ustar Task: Statistics Description: Debian Science Statistics packages This metapackage is part of the Debian Pure Blend "Debian Science" and installs packages related to statistics. This task is a general task which might be useful for any scientific work. It depends from a lot of R packages as well as from other tools which are useful to do statistics. Moreover the Science Mathematics task is suggested to optionally install all mathematics related software. Depends: ess, littler, r-recommended, rkward Why: R utilities or frontends Depends: r-cran-mapproj, r-cran-abind, r-cran-bayesm, \ r-cran-boot, r-cran-cairodevice, r-cran-car, r-cran-chron, \ r-cran-cluster, r-cran-coda, r-cran-codetools, r-cran-date, \ r-cran-dbi, r-cran-rms, r-cran-eco, \ r-cran-effects, r-cran-fbasics, \ r-cran-fcopulae, r-cran-fecofin, r-cran-fextremes, \ r-cran-fmultivar, r-cran-foptions, r-cran-foreign, \ r-cran-fportfolio, r-cran-fseries, r-cran-gdata, r-cran-gmodels, \ r-cran-gplots, r-cran-gregmisc, r-cran-gtools, r-cran-hdf5, \ r-cran-hmisc, r-cran-its, r-cran-kernsmooth, r-cran-lattice, \ r-cran-latticeextra, r-cran-lme4, r-cran-lmtest, r-cran-mapdata, \ r-cran-maps, r-cran-matchit, r-cran-matrix, r-cran-mcmcpack, \ r-cran-mgcv, r-cran-misc3d, r-cran-mnp, r-cran-multcomp, \ r-cran-mvtnorm, r-cran-nlme, r-cran-psy, \ r-cran-qtl, r-cran-quadprog, r-cran-rcmdr, \ r-cran-relimp, r-cran-rggobi, r-cran-rgl, r-cran-rgtk2, \ r-cran-rmetrics, r-cran-rmpi, r-cran-rmysql, r-cran-rodbc, \ r-cran-rpart, r-cran-rpvm, r-cran-rquantlib, r-cran-rserve, \ r-cran-rsprng, r-cran-sandwich, r-cran-sm, r-cran-snow, \ r-cran-strucchange, r-cran-survival, r-cran-tkrplot, \ r-cran-tseries, r-cran-vgam, r-cran-vr, r-cran-xml, \ r-cran-zelig, r-cran-zoo Why: R CRAN Comment: r-cran-rcompgen, r-cran-e1071 These packages formerly mentioned above do not seem to exist. Depends: r-other-gking-matchit Depends: r-cran-msm, r-cran-amore, r-cran-teachingdemos Depends: psignifit, python-stats Depends: python-scipy Why: Provides scipy.stats module Suggests: r-cran-spc Depends: r-cran-vcd Depends: python-statsmodels Suggests: science-mathematics Depends: python-openturns Why: Uncertainty quantification in numerical simulation ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: pandas Homepage: http://pandas.sourceforge.net Language: Python, Cython WNPP: 641464 License: BSD-3 Pkg-URL: http://neuro.debian.net/pkgs/cctools.html Pkg-Description: data structures for "relational" or "labeled" data pandas is a Python package providing fast, flexible, and expressive data structures designed to make working with "relational" or "labeled" data both easy and intuitive. It aims to be the fundamental high-level building block for doing practical, real world data analysis in Python. pandas is well suited for many different kinds of data: . - Tabular data with heterogeneously-typed columns, as in an SQL table or Excel spreadsheet - Ordered and unordered (not necessarily fixed-frequency) time series data. - Arbitrary matrix data (homogeneously typed or heterogeneous) with row and column labels - Any other form of observational / statistical data sets. The data actually need not be labeled at all to be placed into a pandas data structure X-Removed: Packages removed from Debian Depends: r-cran-acepack Pkg-URL: http://snapshot.debian.org/binary/r-cran-acepack/ Homepage: http://cran.us.r-project.org/src/contrib/ Pkg-Description: GNU R package for regression transformations This package provides the functions ace() and avas() for GNU R which can be used to select regression tranformations. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/554512 Depends: r-cran-fcalendar Pkg-URL: http://snapshot.debian.org/binary/r-cran-fcalendar/ Homepage: http://www.Rmetrics.org Pkg-Description: GNU R package for financial engineering -- fCalendar This package of functions for financial engineering and computational finance is part of Rmetrics, a collection of packages written and compiled by Diethelm Wuertz. . fCalendar provides basic time and date manipulations, holiday calculators and other tools. Its code was previously provided within the fBasics package from which it has been split off. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/554513 debian-science-1.0ubuntu1/tasks/highenergy-physics-dev0000644000000000000000000000501312000743562020050 0ustar Task: High Energy Physics (devel) Description: Debian Science High Energy Physics development packages This metapackage will install Debian Science packages related to development of High Energy Physics applications, which is a branch of physics that studies the elementary subatomic constituents of matter and radiation, and their interactions. The field is also called Particle Physics. . You might also be interested in the debtag field::physics and, depending on your focus, in the physics and education-physics metapackages. Depends: cernlib-base-dev, cernlib-core-dev Depends: libclhep-dev Suggests: clhep-doc Depends: libhepmc-dev, libhepmcfio-dev Suggests: hepmc-examples, hepmc-user-manual, hepmc-reference-manual Depends: liblhapdf-dev Suggests: lhapdf-ccwrap-doc Depends: libsiscone-dev, libsiscone-spherical-dev Suggests: siscone-examples, siscone-doc-html, siscone-doc-pdf Depends: libfastjet-dev, libfastjettools-dev, libfastjet-fortran-dev, libfastjetplugins-dev Suggests: fastjet-doc, fastjet-examples Depends: libpythia8-dev, libhepmcinterface-dev Suggests: pythia8-examples, pythia8-doc-html, pythia8-doc-worksheet Depends: fcc, libooptools-dev Depends: libroot-bindings-python-dev, libroot-bindings-ruby-dev, libroot-graf3d-gl-dev, libroot-io-xmlparser-dev, \ libroot-math-mathmore-dev, libroot-math-unuran-dev, libroot-misc-memstat-dev, libroot-misc-table-dev, \ libroot-net-bonjour-dev, libroot-net-ldap-dev, libroot-proof-clarens-dev, libroot-roofit-dev, libroot-geom-dev, \ libroot-graf2d-gpad-dev, libroot-graf2d-graf-dev, libroot-graf2d-postscript-dev, libroot-graf3d-eve-dev, \ libroot-graf3d-g3d-dev, libroot-gui-dev, libroot-gui-ged-dev, libroot-hist-dev, libroot-hist-spectrum-dev, \ libroot-html-dev, libroot-io-dev, libroot-math-foam-dev, libroot-math-genvector-dev, libroot-math-mathcore-dev, \ libroot-math-matrix-dev, libroot-math-minuit-dev, libroot-math-mlp-dev, libroot-math-physics-dev, \ libroot-math-quadp-dev, libroot-math-smatrix-dev, libroot-math-splot-dev, libroot-misc-minicern-dev, \ libroot-montecarlo-eg-dev, libroot-montecarlo-vmc-dev, libroot-net-dev, libroot-net-auth-dev, libroot-proof-dev, \ libroot-proof-proofplayer-dev, libroot-tmva-dev, libroot-tree-dev, libroot-tree-treeplayer-dev, \ libroot-core-dev, libroot-static Depends: librivet-dev, rivet-plugins-dev Suggests: rivet-user-manual, rivet-reference, rivet-plugins-doc Depends: libthepeg-dev Suggests: thepeg-reference Depends: herwig++-dev debian-science-1.0ubuntu1/tasks/viewing0000644000000000000000000000751012114044461015135 0ustar Task: Viewing Description: Debian Science data visualisation packages This metapackage will install Debian Science packages related to data visualization. You might also be interested in the use::viewing debtag. Depends: vistrails Depends: pdl, gnudatalanguage Why: IDL-like Depends: kst Why: displaying scientific data Depends: ifrit Depends: yorick Depends: python-scientific Why: Maybe should go in some other metapackage (mathematics?) Depends: fityk Depends: gnuplot, grace, gri, labplot, graphviz, pyxplot, plotdrop, qtiplot Depends: python-guiqwt Why: collection of widgets based on QWT5 for data visualisation. Depends: imview Depends: mayavi2 Depends: g3data Depends: grits Pkg-Description: Grits is a Virtual Globe library Grits is a "Virtual Globe" library which uses OpenGL to render an image of the earth using satellite and terrain data from publicly accessible servers. This is similar in concept to Google Earth and NASA World Wind, except implemented as a library. Suggests: med-imaging Depends: gwyddion Depends: paraview Depends: visit Homepage: http://www.llnl.gov/visit/ WNPP: 395573 Responsible: Alastair McKinstry Pkg-Description: Interactive parallel visualization and graphical analysis tool Why: Used for 3-D visualisation of netCDF datasets. Depends: gle-graphics Depends: gmsh Suggests: libgtkmathview-bin Suggests: jeuclid-mathviewer Suggests: texlive-pictures Suggests: pgplot5 Why: non-free Suggests: r-cran-plotrix, r-cran-colorspace Suggests: r-cran-aplpack WNPP: 588924 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-cran-aplpack/trunk Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/R/r-cran-aplpack/trunk/ Responsible: Steffen Moeller Homepage: http://cran.r-project.org/web/packages/aplpack License: GPL-2+ Language: R Pkg-Description: Another Plot PACKage for GNU R The package offers a set of functions for drawing special plots. This comprises stem.leaf which plots a stem and leaf plot, the bagplot to plot a 2D variant of boxplots, faces plots chernoff faces, spin3R supports the inspection of a 3D point cloud and there are slider functions for interactive graphics. Suggests: findimagedupes, libpuzzle-bin Why: Those two packages are not necessarily needed for scientific work but a hint for their existence might be very reasonable. Depends: lybniz Depends: 3depict Depends: mathgl Depends: udav Depends: python-viper Suggests: python-matplotlib, python-scitools Depends: matlab2tikz Depends: cassandra Homepage: http://dev.artenum.com/projects/cassandra License: QPL Pkg-Description: VTK/Java based 3D Scientific Data Viewer Cassandra is a open source scientific data viewer based on VTK. Cassandra provides a dynamic interaction with the VTK pipeline and enables to load plugins dynamically in order to perform specific tasks in data manipulation and visualisation. . Cassandra is developed by Artenum in the frame of its internal Research and Development program and illustrates its skills in scientific visualisation and VTK technology. Cassandra has already been used for many applications in scientific computing and space environment analysis. Depends: pgfplots Homepage: http://pgfplots.sourceforge.net/ License: GPLv3 WNPP: 514751 Responsible: OHURA Makoto Pkg-Description: TeX package to draw normal and/or logarithmic plots directly in TeX This package provides tools to generate plots and labeled axes easily. It draws normal plots, logplots and semi-logplots. Axis ticks, labels, legends (in case of multiple plots) can be added with key-value options. It can cycle through a set of predefined line/marker/color specifications. In summary, its purpose is to simplify the generation of high-quality function plots, especially for use in scientific contexts (logplots). Suggests: circos debian-science-1.0ubuntu1/tasks/electrophysiology0000644000000000000000000003700112114044504017245 0ustar Task: Electrophysiology Description: Debian Science packages for Electrophysiology This metapackage will install Debian packages which might be useful for scientists doing electrophysiology-based neuroscience research. . The selection of packages is targeting the application of analysis techniques. Methods developers are referred to the science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging, and med-imaging-dev metapackages for a variety of additional software that might be useful for electrophysiology research. Suggests: science-neuroscience-modeling Suggests: science-dataacquisition Depends: openelectrophy Homepage: http://packages.python.org/OpenElectrophy License: Cecill v2 (GPL-compatible) Language: Python Responsible: NeuroDebian Team WNPP: 556552 Published-Title: OpenElectrophy: an electrophysiological data- and analysis-sharing framework Published-Authors: Samuel Garcia* and Nicolas Fourcaud-Trocmé Published-In: Frontiers in Neuroinformatics, 3:14 Published-Year: 2009 Published-DOI: 10.3389/neuro.11.014.2009 Pkg-Description: data analysis framework for intra- and extra-cellular recordings This package provide a library und GUI for analyzing electrophysiological data. The data handling and storage uses a MySQL-server. The package is written in pure Python. ; Added by blends-inject 0.0.3. [Please note here if modified manually] Suggests: spike Homepage: http://neuroanalysis.org Language: C++, Octave/Matlab Responsible: NeuroDebian Team License: BSD-3 and Academic Free License Pkg-Description: spike train analysis toolbox This toolbox implements several information-theoretic spike train analysis techniques. This implementation behaves like a typical MATLAB toolbox, but the underlying computations are coded in C and optimized for efficiency. Published-Authors: David H. Goldberg, Jonathan D. Victor, Esther P. Gardner, and Daniel Gardner Published-DOI: 10.1007/s12021-009-9049-y Published-In: Neuroinformatics, 7, 165–178 Published-Title: Spike Train Analysis Toolkit: Enabling Wider Application of Information-Theoretic Techniques to Neurophysiology Published-Year: 2009 ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: klustakwik Published-Authors: Kenneth D. Harris, Darrell A. Henze, Jozsef Csicsvari, Hajime Hirase, and György Buzsáki Published-In: Journal of Neurophysiology, 84, 401-414 Published-Title: Accuracy of Tetrode Spike Separation as Determined by Simultaneous Intracellular and Extracellular Measurements Published-Year: 2000 ; Added by blends-inject 0.0.2. [Removed extra information because accepted inside Debian] Depends: libgdf-dev ; Added by blends-inject 0.0.3. [Please note here if modified manually] Suggests: neurodata Homepage: http://sourceforge.net/projects/neurodata/ Language: C++, Octave/Matlab, Perl License: GPL-2+ Pkg-Description: suite to analyze data acquired from electrophysiology experiments Currently, neurodata has an Octave/MATLAB program to analyze electroneurogram traces of coupled oscillators, and a Perl library for the analysis of voltage trace data. ; Added by blends-inject 0.0.3. [Please note here if modified manually] Suggests: qrtailab Why: Useful and used in acquisition/analysis setups Homepage: http://qrtailab.sourceforge.net/ License: LGPL-2 Pkg-Description: Qt-GUI for RTAI QRtaiLab is a QT-based port of the software scope xrtailab of the RTAI project. It can be used as virtual oscilloscope and monitoring application for interacting with the real-time external. ; Added by blends-inject 0.0.7. [now official package] Suggests: stimfit ; Added by blends-inject 0.0.3. [Please note here if modified manually] Suggests: trellis-neuro Homepage: http://sourceforge.net/projects/trellis-neuro/ Language: C, C++ License: GPL-3+ and LGPL-3+ Pkg-Description: interface to neurophysiology data acquisition and stimulation instruments Trellis-Neuro is an Open Source, multi-platform application suite for interfacing with neurophysiology data acquisition and stimulation instruments. It is based on the eXtensible Instrument Processing Protocol (XIPP), QT 4, and C/C++. ; Added by blends-inject 0.0.4. [Please note here if modified manually] Suggests: relacs Homepage: http://www.relacs.net Language: C++ WNPP: 604564 License: GPL-2+ Pkg-Description: framework for closed-loop neurophysiological experiments RELACS is designed as an framework for closed-loop experiments that may considerably speed up this traditional approach and in addition offers novel experimental possibilities. In a closed-loop experiment a stimulus is presented, the resulting response is immediately analyzed, and properties of the next stimulus (e.g. mean intensity) are adjusted as needed. . RELACS comes with an extensive set of data-analysis functions. The functions are implemented in C++ to allow fast and memory efficient data-analysis as it is required for closed-loop experiments: - Basic statistics (e.g. mean, standard deviation) - Spectral analysis: power spectrum, transfer function, coherence - Linear and nonlinear fits (Levenberg-Marquardt and Simplex) - Peak detection - Histograms, interpolation - Stimulus generation: pulse, saw tooth, band-pass filtered white noise, Ornstein-Uhlenbeck noise - Firing rates: mean, binned, convolved with kernels (e.g. rectangle, triangle, Gaussian) - Interspike intervals: histogram, CV, serial correlation, etc. - Spike timing precision: vector strength, reliability, correlation, synchrony etc. . RELACS plugin infrastructure allows to adapt it to specific hardware drivers and they allow you to implement research protocols, filters, spike detectors, etc. ; Added by blends-inject 0.0.4. [Please note here if modified manually] Suggests: chronus Homepage: http://www.chronux.org/ Language: C, Matlab/Octave License: GPL-2+ Pkg-Description: platform for analysis of neural signals Chronux is a Matlab toolbox for signal processing of neural time series data, several specialized mini-packages for spike sorting, local regression, audio segmentation and other tasks. It also includes a graphical user interface (GUI). The current version of the GUI contains a number of features specialised to the analysis of electroencephalography (EEG) data. The eventual aim is to provide domain specific user interfaces (UIs) for each experimental modality, along with corresponding data management tools. Registration: http://www.chronux.org/register/ Remark: last release more than 2 years ago, and no major vital signs since then ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: libbiosig0 Published-Authors: Alois Schlögl, Clemens Brunner Published-DOI: 10.1109/MC.2008.407 Published-In: Computer, 41(10): 44-50 Published-Title: BioSig: A Free and Open Source Software Library for BCI Research Published-URL: http://pub.ist.ac.at/~schloegl/publications/Schloegl2007_BCI_Software.pdf Published-Year: 2008 ; Added by blends-inject 0.0.7. [Package available in Debian - extra information removed] Depends: sigviewer ; Added by blends-inject 0.0.5. [Please note here if modified manually] Suggests: nspike Homepage: http://nspike.sourceforge.net Language: C++ License: GPL-2+ Pkg-Description: electrophysiological and behavioral data collection This project is a electrophysiological and behavioral data collection program that can distribute data collection tasks across multiple machines. It is designed to interface with the NSpike hardware system. Remark: Last vital signs from 2 years ago ; Added by blends-inject 0.0.5. [Please note here if modified manually] Suggests: rtxi Homepage: http://www.rtxi.org Language: C++ License: GPL-2+ Pkg-Description: real-time data acquisition and control applications in biological research The Real-Time eXperiment Interface (RTXI) is a collaborative open-source software development project aimed at producing a real-time Linux based software system for hard real-time data acquisition and control applications in biological research. . Core functionality of RTXI gets extended via plugins, such as - Data Recorder - Virtual Dendrite - Spike-triggered Average - Phase Response Curve - Signal processing ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: bluespike Homepage: https://github.com/globalvariable/BlueSpike Language: C WNPP: 611211 License: GPL-2+ Pkg-Description: Data Acquisition and Neural Spike Processing Software BlueSpike is an electrophysiology tool to perform real-time data acquisition, visualization and sorting of neuronal spikes. It continuously acquires data every 1 ms and realizes digital signal processing on retrieved data. Contains four components: . - KernelSpike: a kernel module. - SpikeViewever - SpikeSorter - Channel Reviewer Published-Authors: Mehmet Kocaturk et al. Published-In: SfN2010, Poster 818.22/OOO43 Published-Title: Real-time experimental interface for electrophysiology experiments Published-Year: 2010 ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: meabench Homepage: http://www.its.caltech.edu/~daw/meabench/ Language: C++ WNPP: 611363 License: GPL-2+ Pkg-Description: tools for recording from MEAs and RT processing Meabench is a set of interacting linux programs for recording data from MEAs and real time processing. It can be used to acquire and visualize data from MultiChannel Systems multi-electrode array hardware in real time. On-line spike detection is available, as well as suppression of artifacts induced by 60 Hz pickup and by stimulation. A growing number of small utilities for data analysis is included with the source code, and you can easily add your own. Meabench provides continuous and triggered recording of raw electrode data as well as extracted spike data. Meabench is very suitable for real-time feedback stimulation, since roundtrip times from pre-amplifier to stimulator is less than 200 ms worst-case (less than 50 ms average). Published-Authors: D. A. Wagenaar, T. B. DeMarse, and S. M. Potter Published-In: Proc. 2nd Int. IEEE EMBS Conf. Neural Eng., 518–521 Published-Title: MEABench: A Toolset for Multi-electrode Data Acquisition and On-line Analysis Published-URL: http://www.its.caltech.edu/~daw/abstracts/05-WDP.html Published-Year: 2005 Remark: 64-bit port is not yet fully tested/supported ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: mclust Homepage: http://redishlab.neuroscience.umn.edu/MClust/MClust.html Language: C/C++, Matlab License: non-DFSG (restrictions: modifications, attribution) Pkg-Description: Matlab toolbox for clustering of electrophysiologic recordings MClust is a toolbox which enables a user to perform automated and manual clustering on single-electrode, stereotrode, and tetrode recordings. It allows manual corrections to automated clustering results. It outputs t-files, which contain (after a header) a list of timestamps in binary format. Timestamps are 32-bit longs at a resolution of 10 timestamps/ms. ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: neo Homepage: http://neuralensemble.org/trac/neo Language: Python WNPP: 659691 Responsible: NeuroDebian Team License: BSD Vcs-Svn: https://neuralensemble.org/svn/neo/ Pkg-Description: IO library for electrophysiological data formats in Python NEO stands for Neural Ensemble Objects and is a project to provide common class names and concepts for dealing with electro-physiological (in vivo and/or simulated) data with the aim of getting OpenElectrophy, NeuroTools, G-node and maybe other projects with similar goals more close together. . In particular Neo provides: . * a set a classes with precise definitions * an IO module that offer a simple API that fit many formats * documentation. * a set of examples like a format convertor Remark: Upstream says not worth packaging before v0.2 is released. Suggests: python-spykeutils ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: pymeg Homepage: https://github.com/badbytes/pymeg/wiki Language: Python License: GPL-3 Pkg-Description: suite for analysis of magnetoencephalography (MEG) data PyMEG is a project in Python to do various neuroimaging processing with magnetoencephalography (MEG) data. The purpose of this project, is to create a suite of functions to do MEG analysis in Python. Remark: Needs DFSG-ification. According to the author is not yet ready for the use by mortals -- wasn't released yet. Depends: libdrawtk-dev Suggests: libxdffileio-dev Suggests: librtfilter-dev Suggests: libeegdev-dev Suggests: libmcpanel-dev Homepage: http://cnbi.epfl.ch/software/mcpanel.html Language: C Responsible: Nicolas Bourdaud License: GPL-3 Pkg-Description: Library providing a scope for multichannel signals mcpanel is a library that provides a scope interface for displaying multichannel signal based on Gtk+. It has been designed to implement easily a realtime display of signal and can be easily integrated in other projects. Suggests: eegview Homepage: http://cnbi.epfl.ch/software/eegview.html Language: C Responsible: Nicolas Bourdaud License: GPL-3 Pkg-Description: Software to display/record EEG signals eegview is a small software to display/record EEG signals. It is particularly useful when used as the acquisition part of a offline protocol or for checking that electrodes are correctly placed... ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: aghermann ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: eeglab Homepage: http://sccn.ucsd.edu/eeglab Language: C, Matlab/Octave WNPP: 605739 Responsible: NeuroDebian Team License: GPL-2+ Pkg-URL: http://neuro.debian.net Pkg-Description: toolbox for processing and visualization of electrophysiological data EEGLAB is an interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data. Published-Authors: Delorme A and Makeig S Published-In: Journal of Neuroscience Methods 134:9-21 Published-Title: EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics Published-Year: 2004 Registration: http://sccn.ucsd.edu/eeglab/install.html ; Added by blends-inject 0.0.7. [Removed extra information about now official package] Suggests: python-neuroshare ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: patchclamp Homepage: http://sourceforge.net/projects/patchclamp Language: C/C++ Responsible: Vadim Alexeenko License: GPL-2+ Pkg-Description: recorder of single-channel and whole-cell currents The ultimate aim is to create an extremely user-friendly software to perform the most common tasks of recording single channels and whole-cell currents ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: spykeview Homepage: https://github.com/rproepp/spykeviewer Language: Python WNPP: 687703 License: promised MIT or BSD-3 Pkg-Description: GUI application for navigating, analyzing and visualizing electrophysiological datasets Based on the neo framework, it works with a wide variety of data formats. Plugin interfaces allow for rapid extension with custom analyses. Remark: Upstream promises public release by SfN 2012 in October debian-science-1.0ubuntu1/tasks/nanoscale-physics0000644000000000000000000002422012264700327017113 0ustar Task: Nanoscale Physics Description: Debian Science Nanoscale Physics packages This metapackage will install Debian Science packages related to Nanoscale Physics, which corresponds to the study of physical systems typically ranging from 1 to 100 nm in size. The properties of such systems usually depend on the number of atoms they are made of, while this number is still relatively large for an accurate description. . The nanoscale is the meeting point of classical and quantum physics. Previous research efforts were considering either smaller systems, for which everybody could develop their own methods and software independently, or much bigger systems, for which it was clearly impossible to provide a fine-grained description. Addressing the issues raised by the nanoscale requires however cooperative and coordinated efforts in a multidisciplinary context. This metapackage is part of such an endeavor. . You might also be interested in the debtag field::physics and, depending on your focus, in the physics and education-physics metapackages. Depends: abinit, mpqc, openmx, psi3, quantum-espresso Depends: drawxtl Depends: etsf-io Depends: feynmf Depends: fityk Depends: gnuplot, grace Depends: horae, ifeffit, sixpack Depends: libblas3gf, liblapack3gf Depends: libfftw3-3 Depends: libgsl0ldbl, gsl-bin Depends: netcdf-bin, netcdf-doc, nco, ncview Depends: openmpi-bin|mpich2|mpich-bin Depends: openmpi-doc|mpich2-doc|mpi-doc Depends: science-numericalcomputation Why: Numerical programming environments similar to Matlab/IDL Depends: avogadro, garlic, gdis, ghemical, v-sim Depends: gwyddion Recommends: axiom, maxima Why: Symbolic maths Recommends: cadabra Recommends: extrema, ggobi, mayavi2, udav Why: Data analysis Recommends: gperiodic, python-elemental Why: Periodic table data Recommends: graphviz Recommends: libblacs-mpi1 Recommends: libscalapack-mpi1 Recommends: python-scientific, python-scipy, python-scitools, python-sympy Why: ODE solvers, optimization algorithms, symbolic maths Recommends: pyxplot Why: publication-quality figures Suggests: dx, dx-doc Suggests: gmsh Why: Support ongoing finite-element projects Suggests: gpiv, gpivtools Suggests: life-apps Why: Partial differential equation library, FEA, CFD Suggests: qtiplot, scidavis Why: Handle file formats used by experimentalists Suggests: science-statistics, science-mathematics Suggests: scilab-sivp Depends: ape Homepage: http://www.tddft.org/programs/APE/ Responsible: Yann Pouillon License: GPL WNPP: 602092 Published-Title: Generating relativistic pseudo-potentials with explicit incorporation of semi-core states using APE, the Atomic Pseudo-potentials Engine Published-Authors: M. J. T. Oliveira, F. Nogueira Published-Year: 2008 Published-In: Computer Physics Communications, 178:524-534 Published-URL: http://dx.doi.org/10.1016/j.cpc.2007.11.003 Published-DOI: 10.1016/j.cpc.2007.11.003 Pkg-Description: Atomic pseudopotential generator APE (Atomic Pseudopotential Engine) is a tool for generating atomic pseudopotentials within the Density-Functional Theory framework. It produces pseudopotential files suitable for use with SIESTA, OCTOPUS and ABINIT. Depends: atompaw Homepage: http://www.wfu.edu/~natalie/papers/pwpaw/man.html Responsible: Yann Pouillon License: GPL WNPP: 602093 Published-Title: A Projector Augmented Wave (PAW) code for electronic structure calculations, Part I: atompaw for generating atom-centered functions Published-Authors: N. A. W. Holzwarth, A. R. Tackett, G. E. Matthews Published-Year: 2001 Published-In: Computer Physics Communications, 178:524-534 Published-URL: http://dx.doi.org/10.1016/S0010-4655(00)00244-7 Published-DOI: 10.1016/S0010-4655(00)00244-7 Pkg-Description: PAW atomic dataset generator The computer program atompaw generates projector and basis functions which are needed for performing electronic structure calculations based on the Projector-Augmented Wave (PAW) method. The program is applicable to materials throughout the periodic table. It produces an output file containing the projector and basis functions and the corresponding matrix elements in a form which can be read be the PWPAW and ABINIT codes. Additional data files are also produced which can be used to help evaluate the accuracy and efficiency of the generated functions. Depends: bigdft Homepage: http://inac.cea.fr/L_Sim/BigDFT/ Responsible: Damien Caliste License: GPL WNPP: 602096 Published-Title: Daubechies wavelets as a basis set for density functional pseudopotential calculations Published-Authors: L. Genovese, A. Neelov, S. Goedecker, T. Deutsch, S. A. Ghasemi, A. Willand, D. Caliste, O. Zilberberg, M. Rayson, A. Bergman, R. Schneider Published-Year: 2008 Published-In: Journal of Chemical Physics, 129:014109 Published-URL: http://link.aip.org/link/?JCP/129/014109 Published-DOI: 10.1063/1.2949547 Pkg-Description: Wavelet-based electronic-structure calculations BigDFT is a DFT-based massively parallel electronic structure code using a wavelet basis set. Wavelets constitute a real space basis set distributed on an adaptive mesh (two levels of resolution in our implementation). . Thanks to our Poisson solver based on a Green function formalism, periodic systems, surfaces and isolated systems can be simulated with the proper boundary conditions. GTH or HGH pseudopotentials are used to remove the core electrons. . The Poisson solver is also integrated in ABINIT, OCTOPUS and CP2K. Depends: cp2k Depends: espresso++ Homepage: http://espresso.scai.fraunhofer.de/ License: Not yet known (hopefully free) Pkg-Description: Extensible Simulation Package for Research on Soft matter ESPResSo is a highly versatile software package for the scientific simulation and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research, with emphasis on charged systems. Depends: exciting Homepage: http://exciting-code.org/ Responsible: Yann Pouillon License: GPL WNPP: 602097 Pkg-Description: All-electron full-potential electronic-structure code exciting is a full-potential all-electron Density-Functional-Theory (DFT) package based on the Linearized Augmented Plane-Wave (LAPW) method. . It can be applied to all kinds of materials, irrespective of the atomic species involved, and also allows for the investigation of the atomic-core region. . We particularly focus on excited state properties, within the framework of time-dependent DFT (TDDFT) as well as within many-body perturbation theory (MBPT). Depends: gpaw Homepage: https://wiki.fysik.dtu.dk/gpaw/ Responsible: Ask Hjorth Larsen License: GPL WNPP: 602748 Published-Title: Real-space grid implementation of the projector augmented wave method Published-Authors: J. J. Mortensen, L. B. Hansen, K. W. Jacobsen Published-Year: 2005 Published-In: Physical Review B, 71:035109 Published-URL: http://prb.aps.org/abstract/PRB/v71/i3/e035109 Published-DOI: 10.1103/PhysRevB.71.035109 Pkg-Description: Real-space PAW-based electronic structure code GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method. It uses real-space uniform grids and multigrid methods or atom-centered basis-functions. Depends: octopus Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page Responsible: Miguel Marques License: LGPL WNPP: 602111 Published-Title: octopus: a tool for the application of time-dependent density functional theory Published-Authors: A. Castro, H. Appel, M. Oliveira, C.A. Rozzi, X. Andrade, F. Lorenzen, M. A. L. Marques, E. K. U. Gross, A. Rubio Published-Year: 2006 Published-In: Physica Status Solidi B, 243:2465-2488 Published-URL: http://hdl.handle.net/10.1002/pssb.200642067 Published-DOI: 10.1002/pssb.200642067 Pkg-Description: Real-space TDDFT-based electronic-structure code Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within Density-Functional Theory (DFT), in its Time-Dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation. Depends: pymca Depends: python-ase Published-Title: An object-oriented scripting interface to a legacy electronic structure code Published-Author: S. R. Bahn and K. W. Jacobsen Published-Year: 2002 Published-In: Computing in Science and Engineering, 4:56-66 Published-URL: http://dx.doi.org/10.1109/5992.998641 Published-DOI: 10.1109/5992.998641 Depends: wannier90 Homepage: http://www.wannier.org/ Responsible: Yann Pouillon License: GPL WNPP: 578829 Published-Title: A Tool for Obtaining Maximally-Localised Wannier Functions Published-Authors: A. A. Mostofi, J. R. Yates, Y.-S. Lee, I. Souza, D. Vanderbilt, N. Marzari Published-Year: 2008 Published-In: Computer Physics Communications, 178:685-699 Published-URL: http://dx.doi.org/10.1016/j.cpc.2007.11.016 Published-DOI: 10.1016/j.cpc.2007.11.016 Pkg-Description: Maximally Localized Wannier Functions Wannier90 is an electronic-structure software computing maximally-localized Wannier functions (MLWF). It works on top of other electronic-structure software, such as Abinit, FLEUR, and PwSCF. Depends: qtoctave Depends: octaviz Pkg-URL: http://snapshot.debian.org/package/octaviz/ Homepage: http://octaviz.sourceforge.net/ Pkg-Description: 3D visualization system for Octave Octaviz is a visualization system for Octave. It is a wrapper that makes all VTK classes accessible from within Octave using the same object-oriented syntax as in C++ or Python. Octaviz also provides high-level functions for 2D and 3D visualization. Using those functions, most common visualization tasks (3D surface plots, contour plots etc) can be accomplished without any knowledge about VTK. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/535537 Depends: fdmnes Pkg-URL: http://people.debian.org/~tille/packages/fdmnes/ debian-science-1.0ubuntu1/tasks/mathematics0000644000000000000000000001266312264700566016004 0ustar Task: Mathematics Description: Debian Science Mathematics packages This metapackage will install Debian Science packages related to Mathematics. You might also be interested in the field::mathematics debtag and, depending on your focus, in the education-mathematics metapackage. Depends: axiom, ginac-tools, xmaxima, wxmaxima Why: Symbolic computations Depends: pari-gp, pari-extra Depends: gap, magnus Why: Group theory Depends: gerris Why: CFD Depends: freefem, freefem3d Depends: freefem++ Suggests: netgen-doc Why: FEA Depends: netgen Why: FEA, mesh generator Depends: gmsh Why: FEA, mesh generator Published-Title: Gmsh: a three-dimensional nite element mesh generator with built-in pre- and post-processing facilities Published-Authors: Christophe Geuzaine and Jean-Francois Remacle Published-In: INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING Published-Year: 2009 Depends: getdp Why: FEA X-Begin-Category: proof assistants X-Comment: According to Hendrik Tews these might end up in a separate metapackage "theorem-proving" or "formal-methods" see http://lists.debian.org/debian-science/2012/05/msg00077.html Depends: coq, proofgeneral Depends: matita, agda, prover9, hol-light, minisat X-End-Category: proof assistants Depends: science-statistics Depends: geomview Depends: octave Depends: xmds Depends: freemat Depends: mathomatic Depends: scilab, scilab-sivp, scilab-scimax, scilab-swt, scilab-ann, scilab-plotlib Depends: regina-normal, snappea Why: Requested by Ben Burton Depends: lp-solve Why: Requested by Aníbal Monsalve Salazar Depends: libmatheval1 Depends: mumps-test Depends: nauty Depends: geogebra Depends: lrslib Suggests: r-cran-evd Depends: python-ffc Depends: kseg Depends: polylib-utils Depends: rheolef Depends: scotch Depends: singular Depends: libgivaro0 Depends: isabelle Remark: upstream prefers Isabelle not being packaged There is an alternative software coq which is packaged in Debian (see above). Depends: bliss Depends: life-apps Why: Partial differential equation library, FEA, CFD Depends: python-openturns Why: Uncertainty quantification in numerical simulation Depends: qtoctave Depends: python-deap Depends: mcl Depends: polybori-gui, polybori X-Removed: Packages removed from Debian Depends: octaviz Pkg-URL: http://snapshot.debian.org/package/octaviz/ Homepage: http://octaviz.sourceforge.net/ Pkg-Description: 3D visualization system for Octave Octaviz is a visualization system for Octave. It is a wrapper that makes all VTK classes accessible from within Octave using the same object-oriented syntax as in C++ or Python. Octaviz also provides high-level functions for 2D and 3D visualization. Using those functions, most common visualization tasks (3D surface plots, contour plots etc) can be accomplished without any knowledge about VTK. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/535537 Depends: sagemath Pkg-URL: http://snapshot.debian.org/package/sagemath/ Homepage: http://sagemath.org/ Pkg-Description: Mathematics software written in Python Sage is a mathematical software package with support for a wide range of mathematics, including algebra, calculus, elementary to very advanced number theory, cryptography, numerical computation, commutative algebra, group theory, combinatorics, graph theory, and exact linear algebra. . Sage integrates several dozen mathematical software packages, making it possible to combine the best algorithms from several different packages together in a single Sage program. . Much of the Sage core and the Sage interfaces are implemented in Cython, helping Sage avoid the usual performance problems associated with Python. . Sage has a friendly command-line interface based on iPython and a web-based notebook interface which can run locally or connect to a remote Sage server over the network. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/573538 Depends: eprover Pkg-URL: http://snapshot.debian.org/package/eprover/1.0.004-1/ Homepage: http://www.eprover.org/ Pkg-Description: Theorem prover for first-order logic with equality E is a fully automatic theorem prover for full first-order logic with equality. It accepts a mathematical specification and, optionally, a hypothesis, and tries to prove the hypothesis and/or find a saturation representing a (counter-)model for the specification. . E is based on a purely equational problem representation and implements a variant of the superposition calculus. Proof search can be guided with a multitude of options or a powerful automatic configuration mode. The system can process input in a number of different formats, including the standard TPTP-2 and TPTP-3 formats. It can generate proof objects in PCL2 or TPTP-3/TSTP format. . E is considered one of the most powerful and friendly automated theorem provers for first-order logic. It has consistently been among the top system in the major categories of the CASC system competition, and usually been the strongest free software system. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/651971 debian-science-1.0ubuntu1/tasks/highenergy-physics0000644000000000000000000000613012000743562017275 0ustar Task: High Energy Physics Description: Debian Science High Energy Physics packages This metapackage will install Debian Science packages related to High Energy Physics, which is a branch of physics that studies the elementary subatomic constituents of matter and radiation, and their interactions. The field is also called Particle Physics. . You might also be interested in the debtag field::physics and, depending on your focus, in the physics and education-physics metapackages. Depends: cernlib, cernlib-base, cernlib-core, cernlib-extras Depends: dzedit Depends: kuipc Depends: kxterm Depends: nypatchy Depends: pawserv Depends: zftp Depends: paw, paw++ Suggests: paw-demos Depends: cernlib-montecarlo Depends: geant321 Suggests: geant321-doc Depends: feynmf Depends: looptools Depends: python-lhapdf, octave-lhapdf Suggests: lhapdf-pdfsets-minimal Depends: root-macro-fastjet Depends: pythia8-root-interface Depends: libroot-bindings-python5.34, libroot-bindings-ruby5.34, libroot-graf3d-gl5.34, libroot-io-xmlparser5.34, \ libroot-math-mathmore5.34, libroot-math-unuran5.34, libroot-misc-memstat5.34, libroot-misc-table5.34, \ libroot-net-bonjour5.34, libroot-net-ldap5.34, libroot-proof-clarens5.34, libroot-roofit5.34, libroot-geom5.34, \ libroot-graf2d-gpad5.34, libroot-graf2d-graf5.34, libroot-graf2d-postscript5.34, libroot-graf3d-eve5.34, \ libroot-graf3d-g3d5.34, libroot-gui5.34, libroot-gui-ged5.34, libroot-hist5.34, libroot-hist-spectrum5.34, \ libroot-html5.34, libroot-io5.34, libroot-math-foam5.34, libroot-math-genvector5.34, libroot-math-mathcore5.34, \ libroot-math-matrix5.34, libroot-math-minuit5.34, libroot-math-mlp5.34, libroot-math-physics5.34, \ libroot-math-quadp5.34, libroot-math-smatrix5.34, libroot-math-splot5.34, libroot-misc-minicern5.34, \ libroot-montecarlo-eg5.34, libroot-montecarlo-vmc5.34, libroot-net5.34, libroot-net-auth5.34, libroot-proof5.34, \ libroot-proof-proofplayer5.34, libroot-tmva5.34, libroot-tree5.34, libroot-tree-treeplayer5.34, \ libroot-core5.34 Depends: root-plugin-graf2d-asimage, root-plugin-geom-gdml, root-plugin-gui-qt, root-plugin-graf2d-qt, \ root-plugin-math-fftw3, root-plugin-math-minuit2, root-plugin-montecarlo-pythia8, root-plugin-net-globus, \ root-plugin-net-krb5, root-plugin-proof-peac, root-plugin-sql-mysql, root-plugin-sql-odbc, \ root-plugin-sql-pgsql, root-plugin-geom-geombuilder, root-plugin-geom-geompainter, root-plugin-graf2d-x11, \ root-plugin-graf3d-x3d, root-plugin-gui-fitpanel, root-plugin-gui-guibuilder, root-plugin-gui-sessionviewer, \ root-plugin-hist-hbook, root-plugin-hist-histpainter, root-plugin-hist-spectrumpainter, root-plugin-io-sql, \ root-plugin-io-xml, root-plugin-math-fumili, root-plugin-tree-treeviewer, root-system-proofd, \ root-system-rootd, root-system-bin, root-system-common, root-system Suggests: root-system-doc Depends: rivet, rivet-plugins, python-rivet, rivet-root-converter Depends: thepeg, thepeg-gui Depends: herwig++ Depends: geant4 debian-science-1.0ubuntu1/tasks/astronomy0000644000000000000000000001730312035753444015533 0ustar Task: Astronomy Description: Debian Science Astronomy packages This metapackage will install Debian Science packages related to Astronomy. You might also be interested in field::astronomy debtag and, depending on your focus, in the education-astronomy metapackage. Depends: gcx Depends: xorsa Why: Celestial Mechanics computations Depends: astronomical-almanac, lightspeed, openuniverse Depends: sextractor Depends: worldwind Depends: wcstools, wcslib-tools, funtools, esorex Depends: gpredict, predict, seesat5 Depends: qfits-tools Depends: yorick-full Suggests: yorick-cubeview, yorick-mira, yorick-spydr, yorick-yao, yorick-svipc, yorick-gyoto Depends: savi Depends: stellarium, xplanet, xplanet-images, celestia, kstars, starplot Depends: lynkeos.app Suggests: sunclock, xtide, xtide-data Why: Took this over from education-astronomy Depends: stardata-common, gliese, yale Depends: boinc-app-milkyway, boinc-app-seti Suggests: scilab-celestlab, scilab-overload, scilab-scimysql X-Comment: It is not really astronomy, do we need another category or should we put space flight related packages into this task? Depends: gyoto Depends: ftools-fv Depends: casacore-tools Depends: xephem Homepage: http://www.clearskyinstitute.com/xephem/ License: Non-free Responsible: Javier Fernandez-Sanguino Pena Pkg-URL: http://snapshot.debian.net/archive/2005/03/13/debian/pool/non-free/x/xephem/ Pkg-Description: An interactive astronomical ephemeris for X. Xephem is an interactive astronomical ephemeris program for X Windows systems with Motif. It provides many graphical views as well as quantitative heliocentric, geocentric and topocentric information for Earth satellites, solar system and celestial objects. . This project used to be an official Debian package in 2002 but vanished from the Debian pool of packaged software (for reasons that should be clarified). The URL of the "unofficial" package points to the location where the old package could be found on http://snapshot.debian.net. . There are later upstream versions than this Debian package available. Ignore: gstar Homepage: http://www.ecn.wfu.edu/~cottrell/gstar/ License: GPL Responsible: Maintainer: Muhammad Hussain Yusuf Pkg-URL: http://snapshot.debian.net/archive/2005/03/13/debian/pool/main/g/gstar/ Pkg-Description: a gtk front-end for the starchart program gstar is a gtk front-end for the "starchart" program (originally by Alan Paeth, updated in 1990 by Craig Counterman) which generates high-quality postscript charts of any chosen region of the sky. It also prints the current Julian date and gives positions of the planets. . This project used to be an official Debian package in 2002 but vanished from the Debian pool of packaged software - perhaps because it is outdated and only reasonable in combination with spacechart. The URL of the "unofficial" package points to the location where the old package could be found on http://snapshot.debian.net. Suggests: pdl, pgplot5, python-scientific Why: Already in science-viewing Depends: orbfit Homepage: http://newton.dm.unipi.it/orbfit/ WNPP: 459154 License: GPL Responsible: Steffen Moeller Pkg-Description: computation of asteroidal orbits OrbFit is a software system allowing one to compute the orbits of asteroids (soon also comets) starting from the observations, to propagate these orbits, and to compute predictions on the future (and past) position on the celestial sphere. It is a tool to be used to find a well known asteroid, to recover a lost one, to attribute a small group of observations, to identify two orbits with each other, to study the future (and/or past) close approaches to Earth, thus to assess the risk of an impact, and more. . OrbFit has been developed by a team of professional scientists, working in the field of asteroid and comet dynamics, orbit determination, nonlinear and chaotic dynamics, and astrometry. The composition of the OrbFit consortium, and the motivations for this work, are described below. . Status of packaging: . A rudimentary package was prepared, upstream was contacted with a very positive reply. The packaging bits will be injected to pkg-scicomp in near future. Depends: linoccult Homepage: http://linoccult.sourceforge.net/ WNPP: 459358 License: GPL Responsible: Steffen Moeller Pkg-Description: predicts occultations of stars by minor planets LinOccult uses the DE405 precomputed major planets ephemeris (position of astronomical object in the sky at a given time) that are provided by the Jet Propulsion Laboratory (JPL) for a precise numerical integration of asteroidal orbits. The user can select asteroids to process by changing several parameters in a configuration file. . Some initial packaging has been performed and will be submitted to pkg-scicomp.alioth.debian.org. Depends: midas Homepage: http://www.eso.org/sci/data-processing/software/esomidas/ WNPP: 412488 License: GPL Responsible: Alastair McKinstry Pkg-Description: the European Southern Observatory Munich Image Data Analysis System The ESO-MIDAS system provides general tools for image processing and data reduction with emphasis on astronomical applications including imaging and special reduction packages for ESO instrumentation at La Silla and the VLT at Paranal. In addition it contains applications packages for stellar and surface photometry, image sharpening and decomposition, statistics and various others. . The official name, ESO-MIDAS, is a registered trademark. ESO-MIDAS is available under the GNU General Public License (GPL), and can be implemented on OpenVMS and UNIX (Linux) systems. Depends: heasoft-fv Depends: saods9 Depends: ssystem Pkg-URL: http://snapshot.debian.org/package/ssystem/ Homepage: http://www1.las.es/~amil/ssystem Pkg-Description: 3D solar system simulator An OpenGL Solar System simulator which includes the sun, the nine planets, a few major satellites, and background stars. . This package has since been rewritten and repackaged as Celestia, but since that package has significantly higher hardware requirements than ssystem does, this package is being kept around. Celestia has a better looking solar system, more options, and unlike ssystem, is actually still being worked on, so you probably only want to use this if you have older hardware that cannot run Celestia at a reasonable speed. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/352709 Suggests: stars Pkg-URL: http://snapshot.debian.org/package/stars/ Homepage: http://www.aoc.nrao.edu/~wbrisken/src/ Pkg-Description: star map program that draws the night sky Stars is an astronomy program that lets you view the sky from your computer. . Except for generating a small rotation matrix and some parameters, all math is integer based, allowing very fast display. At 16 bytes of memory per object, many objects can be loaded at once. Most graphics are antialiased. Depends: spacechart Homepage: http://www.gnu.org/software/spacechart/ Pkg-URL: http://snapshot.debian.org/package/spacechart/ Pkg-Description: Star map viewer and navigator SpaceChart is a program to display 3d maps of stars and move freely around it. It is capable of showing only a subset of the stars in a given data file, and only those within a given distance of the center of the display. Also, it shows lines between stars that are closer than a given distance. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/460795 debian-science-1.0ubuntu1/tasks/biology0000644000000000000000000000205011556544023015133 0ustar Task: Biology Description: Debian Science Biology packages This metapackage will install Debian Science packages related to Biology. You might also be interested in the field::biology debtag. . This metapackage makes use of the packages med-bio and med-bio-dev (for development of biological applications) which are maintained by Debian Med - another Debian Pure Blend. If you are a biologist you are most probably interested in the Debian Med project which deals with biology and medicine in much more detail then the more general Debian Science. Depends: med-bio Meta-Depends: svn://svn.debian.org/blends/projects/med/trunk/debian-med/tasks/bio Remark: Maintained by Debian Med Blend For more information see http://debian-med.alioth.debian.org/tasks/bio Suggests: med-bio-dev Meta-Suggests: svn://svn.debian.org/blends/projects/med/trunk/debian-med/tasks/bio-dev Remark: Maintained by Debian Med Blend For more information see http://debian-med.alioth.debian.org/tasks/bio-dev Depends: bauble Depends: genesis, avida-base Depends: critterding debian-science-1.0ubuntu1/tasks/geography0000644000000000000000000000664612264700327015471 0ustar Task: Geography Description: Debian Science Geography packages This metapackage will install Debian Science packages related to Geography. You might also be interested in the field::geography debtag and, depending on your focus, in the education-geography metapackage. Depends: gis-workstation Why: handled by Debian GIS. The Depends: will be replaced by an other special \ tag (its name to be decided). Depends: grass Depends: qgis Depends: qgis-plugin-grass Depends: proj-bin Depends: mapserver-bin, \ gmt, \ gpsbabel, \ gpx2shp, \ gpsd, \ gpsdrive, \ gpsman, \ earth3d, \ openscenegraph, \ thuban, \ drawmap, \ gpstrans, \ geoip-bin, \ gpsd-clients, \ grass-doc, \ php5-mapscript, \ phppgadmin, \ gpsmanshp, \ viking, \ avce00, \ e00compr, \ gdal-bin, \ ogdi-bin Comment: kflog was removed from Debian in Lenny and is not really a good candidate for Debian Science so it makes no sense to add it as prospective package here. Depends: postgis, postgresql-9.3-postgis Depends: osm2pgsql Suggests: googleearth-package Depends: josm, \ josm-plugins, \ merkaartor, \ gosmore, \ python-mapnik2, \ mapnik-utils, \ osmpbf-bin, \ imposm Suggests: sumo X-Depends: osmarender Why: Hmmm, was there any package? I just can find http://wiki.openstreetmap.org/index.php/Osmarender but no download information etc. Depends: r-cran-sp, r-cran-maptools, r-cran-mapdata, r-cran-mapproj, r-cran-maps Depends: pgadmin3 Depends: openjump Pkg-URL: http://snapshot.debian.org/package/openjump/ Homepage: http://jump-pilot.sourceforge.net/ Pkg-Description: Open Java Unified Mapping Platform JUMP The Open Java Unified Mapping Platform (JUMP) is a GUI-based application for viewing and processing spatial data. It includes many common spatial and GIS functions. . OpenJUMP has the following features: * provides viewing, editing, and processing spatial datasets * provides an API giving full programmatic access * loading map data using WMS * is highly modular and extensible Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/626716 Suggests: grace6 Pkg-URL: http://snapshot.debian.org/package/grace6/ Homepage: http://plasma-gate.weizmann.ac.il/Grace/ Pkg-Description: An XY plotting tool Grace is a point-and-click tool that allows the user to draw X-Y plots. This is the program formerly known as Xmgr. . A few of its features are: User defined scaling, tick marks, labels, symbols, line styles, colors. Polynomial regression, splines, running averages, DFT/FFT, cross/auto-correlation. Batch mode for unattended plotting. Hardcopy support for PostScript, FrameMaker and several image formats. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/459484 X-Depends: renderathome, osm-tools X-Comment: These packages never existed and its totally inclear what was meant Any information about this? debian-science-1.0ubuntu1/tasks/nanoscale-physics-dev0000644000000000000000000001453512000373313017664 0ustar Task: Nanoscale Physics Development Description: Debian Science Nanoscale Physics development packages This metapackage will install Debian Science packages which might be helpful for the development of applications for Nanoscale Physics. . You might also be interested in the debtag field::physics and, depending on your focus, in the nanoscale-physics, physics and education-physics metapackages. Depends: abinit-doc Why: Abinit input parser and symmetry finder Depends: libblas-dev, libblas-doc, liblapack-dev, liblapack-doc Depends: libetsf-io-dev, libetsf-io-doc Depends: libfftw3-dev, libfftw3-doc Depends: libgsl0-dev, gsl-bin, gsl-doc-info, gsl-ref-html|gsl-ref-psdoc Depends: libnetcdf-dev, netcdf-doc Depends: libtrilinos-dev, libtrilinos-doc Why: High-performance computing Depends: libxc-dev WNPP: 602110 Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc Responsible: Yann Pouillon License: LGPL Language: C, Fortran 90 Pkg-Description: Library of DFT exchange-correlation functionals Libxc is a library of exchange-correlation functionals. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals that can be used by all the ETSF codes and also other codes. . In libxc you can find different types of functionals: LDA, GGA, hybrids, mGGA (experimental) and LCA (not working). This functionals depend on local information, in the sense that the value of the potential at a given point depends only on the values of the density - and the gradient of the density and the kinetic energy density, for the GGA and mGGA cases, or the vorticity for LCA - at a given point. . As of today, more than 100 functionals are available for various kinds of electronic-structure calculations. Remark: Library will probably be released with different name because the name is just taken (see WNPP bug) Depends: wannier90-dev WNPP: 578829 Responsible: Yann Pouillon Homepage: http://www.wannier.org/ License: GPL Language: Fortran 90 Pkg-Description: Maximally Localized Wannier Functions - Development files Wannier90 is an electronic-structure software computing maximally-localized Wannier functions (MLWF). It works on top of other electronic-structure software, such as Abinit, FLEUR, and PwSCF. . This package contains the development files needed to interface other software with Wannier90. Recommends: gsl-doc-pdf Recommends: libblacs-mpi-dev Recommends: libscalapack-mpi-dev, scalapack-doc Recommends: science-mathematics-dev Suggests: liblife-dev Why: Partial differential equation library, FEA, CFD Suggests: opencascade-draw Depends: libopencascade-dev Suggests: python-netcdf Depends: libfox95 Homepage: http://www1.gly.bris.ac.uk/~walker/FoX/ Responsible: Yann Pouillon License: BSD-like WNPP: 602100 Pkg-Description: A Fortran library for XML FoX is an XML library written in Fortran 95. It allows software developers to read, write and modify XML documents from Fortran applications without the complications of dealing with multi-language development. . The developer is offered three principle APIs which are accessed as Fortran modules. FoX_wxml is an XML writer used to sequentially create arbitrary XML documents quickly with minimal memory requirements. FoX_sax is a streaming, validating parser based on java's Simple API for XML. The third module, FoX_dom, offers a full implementation of the W3C Document Object Model (DOM). Depends: libnbc Homepage: http://www.unixer.de/research/nbcoll/libnbc/ Responsible: Yann Pouillon License: BSD WNPP: 602104 Published-Title: Implementation and Performance Analysis of Non-Blocking Collective Operations for MPI Published-Authors: T. Hoefler, A. Lumsdaine, W. Rehm Published-Year: 2007 Published-In: Proceedings of the 2007 International Conference on High Performance Computing, Networking, Storage and Analysis, SC07 Published-URL: http://www.unixer.de/publications/?pub=46 Published-DOI: 10.1145/1362622.1362692 Pkg-Description: Non-Blocking MPI Collective Operations LibNBC is a prototypic implementation of a nonblocking interface for MPI collective operations. Based on ANSI C and MPI-1, it supports all MPI-1 collective operations in a nonblocking manner. Depends: libpspio Homepage: http://www.tddft.org/trac/libpspio/ Responsible: Yann Pouillon License: LGPL WNPP: 640664 Pkg-Description: Library to read and write pseudopotentials Pseudopotentials consist in atomic data used for atomic-scale electronic structure calculations. Libpspio is a library to read and write pseudopotentials in various formats, allowing as well for conversion in some cases. Depends: libxc Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc Responsible: Damien Caliste License: LGPL WNPP: 602110 Pkg-Description: Library of DFT exchange-correlation functionals Libxc is a library of exchange-correlation functionals. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals that can be used by all the ETSF codes and also other codes. . In libxc you can find different types of functionals: LDA, GGA, hybrids, mGGA (experimental) and LCA (not working). This functionals depend on local information, in the sense that the value of the potential at a given point depends only on the values of the density - and the gradient of the density and the kinetic energy density, for the GGA and mGGA cases, or the vorticity for LCA - at a given point. . As of today, more than 100 functionals are available for various kinds of electronic-structure calculations. Depends: spglib Homepage: http://sourceforge.net/projects/spglib/ Responsible: Yann Pouillon License: BSD WNPP: 602113 Pkg-Description: Crystal symmetry finder library Spglib is a C-library written for finding crystal symmetry. Symmetry operations, space groups, ..., can be obtained using this symmetry finder. Depends: root-system Depends: libroot-tmva-dev, libroot-montecarlo-vmc-dev, libroot-math-mlp-dev X-Comment: Somebody injected the libraries from the ROOT system explicitely here - so these are included since root-system is packaged again X-Suggests: root-plugin-fftw3, libroot-mathmore5.18 In case these packages will be created in root-system these need to be added here as well. debian-science-1.0ubuntu1/tasks/dataacquisition-dev0000644000000000000000000000052311654724642017436 0ustar Task: Data acquisition development Description: Debian Science data acquisition development packages This metapackage will install Debian Science packages which are helpful to develop applications related to data acquisition. This might be used in several sciences. Depends: libnarval1-dev Depends: libtango7-dev, liblog4tango4-dev debian-science-1.0ubuntu1/tasks/astronomy-dev0000644000000000000000000000121412131205172016264 0ustar Task: Astronomy-dev Description: Debian Science Astronomy-dev packages This metapackage will install Debian Science packages which might be helpful for development of applications for Astronomy. . You might also be interested in the science-astronomy metapackage. Depends: libnova-dev Depends: libworldwind-java Depends: libccfits-dev, libcfitsio3-dev, python-pyfits, libqfits-dev, slang-cfitsio, libastro-fits-cfitsio-perl Depends: libsofa-c-dev, libstarlink-pal-dev, libstarlink-ast-dev, libwcstools-dev, wcslib-dev, libcpl-dev Depends: python-pywcs, python-cpl Depends: python-astropy-legacy Depends: libgyoto0-dev Depends: casacore-dev debian-science-1.0ubuntu1/tasks/chemistry0000644000000000000000000002054512131260702015474 0ustar Task: Chemistry Description: Debian Science Chemistry packages This metapackage will install Debian Science packages related to Chemistry. You might also be interested in the field::chemistry debtag and, depending on your focus, in the education-chemistry metapackage. Why: To be handled by debichem once they have metapackages (like \ science-geography / Debian GIS and science-biology / Debian Med) Depends: apbs, bkchem, bodr, libcdk-java, chemeq, \ chemical-mime-data, chemtool, easychem, gabedit, galculator, \ garlic, gausssum, gchempaint, gdis, ghemical, gcrystal, gcu-bin, \ gcu-plugin, gperiodic, \ gromacs | gromacs-lam | gromacs-mpich | gromacs-openmpi, \ kalzium, katomic, mopac7-bin, mpqc, mpqc-support, \ openbabel, python-openbabel, psi3, pymol, \ viewmol, xdrawchem, xmakemol-gl | xmakemol, v-sim Why: from the DebianScience/Chemistry wiki page Depends: rasmol Registration: http://www.rasmol.org/register.shtml Depends: adun.app Why: 3D viewer and calculation output visualisation Depends: gdpc Depends: xbs Depends: gelemental Suggests: gdpc-examples Depends: avogadro Depends: gamgi Depends: massxpert Depends: drawxtl Depends: chemical-structures Depends: freefoam Depends: pyfai Depends: libegad Homepage: http://egad.ucsd.edu/egad/ WNPP: 429693 License: LGPL Responsible: LI Daobing Pkg-Description: rational protein design library The EGAD Library is a modular, object oriented approach to rational protein design. It is platform-independent, written in C++ and, most importantly, free. Its raison d'etre is to serve as a tool for building protein design applications. It can also be used as a test-bed for the comparison of different energy functions and minimization algorithms under the same physical model. . Citations of EGAD Library should reference the paper in the Journal of Computational Chemistry. doi:10.1002/jcc.20727 Depends: libint Homepage: http://www.chem.vt.edu/chem-dept/valeev/software/libint/libint.html WNPP: 425039 License: GPL Responsible: Daniel Leidert Pkg-Description: Evaluate the integrals in modern atomic and molecular theory Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. The idea of the library is to let computer write optimized code for computing such integrals. There are two primary advantages to this: much less human effort is required to write code for computing new integrals, and code can be optimized specifically for a particular computer architecture (e.g., vector processor). . Libint has been utilized to implement methods such as Hartree-Fock (HF) and Kohn-Sham density functional theory (KS DFT), second-order Moller-Plesset perturbation theory (MP2), coupled cluster singles and doubles (CCSD) method, as well as explicitly correlated R12 methods. The following software packages use Libint: . Improves mpqc (#409025) and psi3. Depends: molden Homepage: http://www.cmbi.ru.nl/molden/ License: non-free Responsible: Debichem Team Pkg-URL: http://svn.debian.org/wsvn/debichem/wnpp/molden/?rev=0&sc=1 Pkg-Description: processing program of molecular and electronic structure MOLDEN is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the MOLDEN Format. MOLDEN reads all the required information from the GAMESS / GAUSSIAN outputfile. MOLDEN is capable of displaying Molecular Orbitals, the electron density and the Molecular minus Atomic density. Either the spherically averaged atomic density or the oriented ground state atomic density can be subtracted for a number of standard basis sets. MOLDEN supports contour plots, 3-d grid plots with hidden lines and a combination of both. It can write a variety of graphics instructions; postscript, X, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure. The X version of MOLDEN is also capable of importing and displaying of chemx, PDB, and a variety of mopac/ampac files and lots of other formats. It also can animate reaction paths and molecular vibrations. It can calculate and display the true or Multipole Derived Electrostatic Potential and atomic charges can be fitted to the Electrostatic Potential calculated on a Connolly surface. MOLDEN has a powerful Z-matrix editor which give full control over the geometry and allows you to build molecules from scratch, including polypeptides. MOLDEN was also submitted to the QCPE (QCPE619), allthough the X version is considerably running behind on the current one. Depends: molekel Homepage: http://bioinformatics.org/molekel/ License: GPL-2+ Responsible: Michael Banck Pkg-URL: http://svn.debian.org/wsvn/debichem/wnpp/molekel/?rev=0&sc=1 Pkg-Description: Advanced Interactive 3D-Graphics for Molecular Sciences Depends: tinker Homepage: http://dasher.wustl.edu/tinker/ License: non-free Responsible: LI Daobing Pkg-URL: http://svn.debian.org/wsvn/debichem/wnpp/tinker/?rev=0&sc=1 Pkg-Description: Software Tools for Molecular Design The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L), Liam Dang's polarizable potentials, and our own AMOEBA polarizable atomic multipole force field. Parameter sets for other standard force fields such as GROMOS, UFF, ENCAD and MM4 are under consideration for future releases. . The TINKER package includes a variety of novel algorithms such as a new distance geometry metrization method that has greater speed and better sampling than standard methods, Elber's reaction path methods, several of our Potential Smoothing and Search (PSS) methods for global optimization, an efficient potential surface scanning procedure, a flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, a selection of continuum solvation treatments including several variants of the generalized Born (GB/SA) model, an efficient truncated Newton (TNCG) local optimizer, surface areas and volumes with derivatives, a simple free energy perturbation facility, normal mode analysis, minimization in Cartesian, torsional or rigid body space, velocity Verlet stochastic dynamics, an improved spherical energy cutoff method, Particle Mesh Ewald summation for partial charges and regular Ewald for polarizable multipoles, a novel reaction field treatment of long range electrostatics, and more.... Depends: jmol Depends: qutemol Depends: cp2k Depends: pdb2pqr Depends: mmass, mmass-modules Depends: python-mzml Suggests: python-mzml-doc Depends: tandem-mass Depends: openchrom Homepage: http://www.openchrom.net/ License: EPL Pkg-Description: process chromatographic and mass spectrometric data OpenChrom is an open source software for chromatography based on the Eclipse Rich Client Platform (RCP). Its focus is to handle mass spectrometry systems (e.g. GC/MS, LC/MS, Py-GC/MS, HPLC-MS) data files natively. OpenChrom is able to import binary and textual chromatographic data files, such as *.D chromatograms from Agilent Technologies or NetCDF. Moreover, it offers a nice graphical user interface and is available for various operating systems, e.g. Windows, Linux, Solaris and Mac OSX. A basis set of methods to detect baselines, peaks and to integrate peaks in a chromatogram are implemented. Preprocessing steps, e.g. to remove certain mass fragments (m/z) such as nitrogen (28) or water (18), are supported by applying filter on the chromatogram or mass spectrum. Extensions are welcome, as OpenChrom is open source and uses a flexible approach, which allows others to implement their own methods, algorithms, filters, detectors or integrators. Therefore, OpenChrom shall be an efficiently system to process chromatographic and mass spectrometric data using an extensible and flexible plugin approach. Depends: fdmnes Pkg-URL: http://people.debian.org/~tille/packages/fdmnes/ debian-science-1.0ubuntu1/tasks/simulations0000644000000000000000000000116212000002774016024 0ustar Task: Simulations Description: Debian Science Simulation packages This metapackage will install Debian Science packages that are used to do simulations in different fields of science. Depends: sumo Depends: esys-particle, lammps, liggghts, yade Depends: python-deap Depends: freefoam Depends: getdp Published-Authors: P. Dular and C. Geuzaine and A. Genon and W. Legros Published-Title: An evolutive software environment for teaching finite element methods in electromagnetism Published-In: IEEE Transactions on Magnetics Published-Year: 1999 Depends: fdmnes Pkg-URL: http://people.debian.org/~tille/packages/fdmnes/ debian-science-1.0ubuntu1/tasks/engineering0000644000000000000000000001264512000002774015757 0ustar Task: Engineering Description: Debian Science Engineering packages This metapackage is part od the Debian Pure Blend "Debian Science" and installs packages related to Engineering. . Please not that there is an additional package engineering-dev which depends from packages which are useful to develop engineering related software. Depends: librecad Depends: sailcut Why: CAD software for design of sails Depends: opencascade-draw Depends: python-silo, libsilo-bin Depends: gerris Depends: gmsh Published-Title: Gmsh: a three-dimensional nite element mesh generator with built-in pre- and post-processing facilities Published-Authors: Christophe Geuzaine and Jean-Francois Remacle Published-In: INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING Published-Year: 2009 Depends: getdp Published-Authors: P. Dular and C. Geuzaine and A. Genon and W. Legros Published-Title: An evolutive software environment for teaching finite element methods in electromagnetism Published-In: IEEE Transactions on Magnetics Published-Year: 1999 Depends: netgen Depends: pythoncad Depends: z88 Depends: freecad Depends: life-apps Depends: python-openturns Depends: code-aster-gui Depends: code-saturne, ecs Depends: hdfview Depends: syfi-bin Depends: cba Depends: python-fiat Suggests: r-cran-spc Depends: syrthes Depends: freefoam Depends: brlcad Homepage: http://my.brlcad.org/ WNPP: 289632 License: GPL Responsible: none Pkg-Description: A Combinatorial/Constructive Solid Geometry, solid modeling system BRL-CAD is a powerful Combinatorial/Constructive Solid Geometry (CSG) solid modeling system that includes an interactive geometry editor, ray-tracing support for rendering and geometric analysis, network-distributed framebuffer support, image and signal-processing tools, and an embedded scripting language. It has been developed over a 20 year period and is now a stable mature product. This is the first GPL'ed release of the package. It is being maintained by the US Army Research laboratory (ARL). Depends: avl Homepage: http://web.mit.edu/drela/Public/web/avl/ WNPP: 513608 License: GPL Responsible: "Loïc Fejoz" Pkg-Description: Analyser for the aerodynamic and flight-dynamic of rigid aircraft. AVL is a program for the aerodynamic and flight-dynamic analysis of rigid aircraft of arbitrary configuration. It employs an extended vortex lattice model for the lifting surfaces, together with a slender-body model for fuselages and nacelles. General nonlinear flight states can be specified. The flight dynamic analysis combines a full linearization of the aerodynamic model about any flight state, together with specified mass properties. Depends: cgns-convert Depends: pycgns Homepage: http://elsa.onera.fr/CGNS/releases/ License: GPL-2 Pkg-Description: Package is a Python binding to the CGNS library The package contains a wrapper on top of the ADF and MLL APIs, some tools, demos, tests, and examples taken from the CGNS tutorial. X-Removed: Packages removed from Debian Depends: varkon Homepage: http://varkon.sourceforge.net Pkg-URL: http://snapshot.debian.org/package/varkon/ Pkg-Description: A CAD-system with parametric modelling VARKON is a high level development tool for applications in the area of Engineering, Computer Aided Design and Product Modelling. . VARKON can be used as a traditional CAD-system with drafting, modelling and visualisation if you want to but the real power of VARKON is in parametric modelling and CAD applications development. VARKON includes interactive parametric modelling in 2D or 3D but also the unique MBS programming language integrated in the graphical environment. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/596115 Depends: tochnog Homepage: http://tochnog.sourceforge.net/ Pkg-URL: http://snapshot.debian.org/package/tochnog/ Pkg-Description: A free implicit/explicit finite element analysis program Tochnog is a program for finite element analysis. Multithreading and multiprocessor systems are supported. Here is a partial list of models supported: * Differential equations (materials). * Convection-diffusion equations, * Stokes and Navier-Stokes, * Elasticity (isotropy and transverse isotropy), * Plasticity (Von-Mises, Mohr-Coulomb, Gurson, etc.; plasticity surfaces can be arbitrarily combined). . Residues in equations and error estimates for all data can be printed/plotted. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/503504 Depends: salome Homepage: http://www.salome-platform.org/ Pkg-URL: http://snapshot.debian.org/package/salome/ Pkg-Description: Numerical simulation pre- and post-processor Salomé is a pre- and post-processor for numerical simulations. It can import CAD files in IGES and STEP formats, facilitates component integration in heterogeneous systems, and has a user-friendly GUI as well as a Python console with all of the platform functionality. . This package contains the Salomé core runtime binaries, private libraries, and python files comprising a basic Salomé installation. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/657433 debian-science-1.0ubuntu1/tasks/neuroscience-cognitive0000644000000000000000000005277412121070204020140 0ustar Task: Cognitive Neuroscience Description: Debian Science packages for Cognitive Neuroscience This metapackage will install Debian packages which might be useful for scientists doing cognitive neuroscience research. This comprises the full research process from conducting psychophysical experiments, over data acquisition and analysis, to visualization and typesetting of scientific results. . The selection of packages is targeting the application of analysis techniques. Methods developers are referred to the science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging, and med-imaging-dev metapackages for a variety of additional software that might be useful in the context of cognitive neuroscience. Suggests: science-typesetting Meta-Suggests: svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/typesetting Suggests: science-psychophysics Meta-Suggests: svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/psychophysics Depends: psignifit Why: Psychometric function fitting. Depends: amide Why: Flexible volume slicing and rendering. Published-Title: AMIDE: A Free Software Tool for Multimodality Medical Image Analysis Published-Authors: Andreas M. Loening, Sanjiv S. Gambhir Published-In: Molecular Imaging, 2: 131-137 Published-Year: 2003 Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/14649056 Published-DOI: Depends: dicomnifti Why: Fully automated DICOM-to-NIfTI converter. Depends: minc-tools, medcon, xmedcon, nifti-bin Why: Misc. image handling tools Depends: python-nifti Why: Python IO library for the NIfTI format. Depends: fsl Why: Comprehensive MRI analysis suite. Registration: http://www.fmrib.ox.ac.uk/fsldownloads/ Published-Title: Advances in functional and structural MR image analysis and implementation as FSL Published-Authors: S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, P.M. Matthews Published-In: NeuroImage, 23:208-219 Published-Year: 2004 Published-URL: http://dx.doi.org/10.1016/j.neuroimage.2004.07.051 Published-DOI: 10.1016/j.neuroimage.2004.07.051 Depends: fslview Registration: http://www.fmrib.ox.ac.uk/fsldownloads/ Published-Title: Advances in functional and structural MR image analysis and implementation as FSL Published-Authors: S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, P.M. Matthews Published-In: NeuroImage, 23:208-219 Published-Year: 2004 Published-URL: http://dx.doi.org/10.1016/j.neuroimage.2004.07.051 Published-DOI: 10.1016/j.neuroimage.2004.07.051 Depends: python-mvpa Why: Framework for multivariate pattern analysis of neuroimaging datasets. Published-Title: PyMVPA: a unifying approach to the analysis of neuroscientific data Published-Authors: Michael Hanke, Yaroslav O. Halchenko, Per B. Sederberg, Emanuele Olivetti, Ingo Fründ, Jochem W. Rieger, Christoph S. Herrmann, James V. Haxby, Stephen José Hanson, Stefan Pollmann Published-In: Frontiers in Neuroinformatics, 3:3 Published-Year: 2009 Published-URL: http://www.frontiersin.org/neuroinformatics/paper/10.3389/neuro.11/003.2009/ Published-DOI: 10.3389/neuro.11.003.2009 Depends: caret Why: Cortical reconstruction and volume-to-surface mapping. Published-Title: An Integrated Software Suite for Surface-based Analyses of Cerebral Cortex Published-Authors: David C. Van Essen, Heather A. Drury, James Dickson, John Harwell, Donna Hanlon, Charles H. Anderson Published-In: Journal of American Medical Informatics Association, 8(5): 443-459 Published-Year: 2001 Published-URL: http://www.pubmedcentral.nih.gov/articlerender.fcgi?pubmedid=11522765 Depends: python-pyepl Why: Library to write and run psychological experiments. Published-Title: PyEPL: A cross-platform experiment-programming library Published-Authors: Aaron S. Geller, Ian K. Schleifer, Per B. Sederberg, Joshua Jacobs, Michael J. Kahana Published-In: Behavioral Research Methods, 39: 950-958 Published-Year: 2007 Published-URL: http://prdownloads.sourceforge.net/pyepl/pyepl_brmic.pdf?download Depends: praat Why: Speech synthesis and analysis -- standard tool for auditory stimulus generation. Depends: slicer Published-Title: 3D SLICER Published-Authors: Steven Pieper, Michael Halle, Ron Kikinis Published-In: Proceedings of the 1st IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 1:632-635 Published-Year: 2004 Published-URL: http://www.slicer.org/publications/item/view/91 Depends: dicom3tools Why: Supports conversion from proprietary formats, such as GE into DICOM. Depends: voxbo Registration: http://voxbo.org/usage.html Depends: bioimagesuite Homepage: http://www.bioimagesuite.org/ License: GPL Pkg-Description: integrated image analysis software suite BioImage Suite has extensive capabilities for both neuro/cardiac and abdominal image analysis and state of the art visualization. Many packages are available that are highly extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. It can be integrated with other biomedical image processing software, such as FSL and SPM. This site provides information, downloads, documentation, and other resources for users of the software. . BioImage Suite was developed at Yale University and has been extensively used at different labs at Yale since 2004. . There is a forum at BioImage Suite site for discussion of compiling it from source and packaging issues at http://research.yale.edu/bioimagesuite/forum/index.php?board=12.0 Depends: afni Homepage: http://afni.nimh.nih.gov/ WNPP: 409849 Responsible: Michael Hanke License: GPL Pkg-URL: http://neuro.debian.net/pkgs/afni.html Pkg-Description: environment for processing and displaying functional MRI data AFNI is an environment for processing and displaying functional MRI data. It provides a complete analysis toolchain, including 3D cortical surface models, and mapping of volumetric data (SUMA). In addition to its own format AFNI understands the NIfTI format and is therefore easily usable in combination with FSL and Freesurfer. Published-Title: AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages Published-Authors: Robert W. Cox Published-In: Computers and Biomedical Research, 29:162-173 Published-Year: 1996 Published-URL: http://afni.nimh.nih.gov/pub/dist/doc/papers/afni_paper1.pdf Depends: mni-autoreg Homepage: http://www.bic.mni.mcgill.ca/software/mni_autoreg/ License: no-free, but GPLed parts Responsible: Michael Hanke Pkg-URL: http://apsy.gse.uni-magdeburg.de/debian/pool/contrib/m/mni-autoreg-model/ Pkg-Description: MNI average brain (305 MRI) stereotaxic registration model This package provides a version of the MNI Average Brain (an average of 305 T1-weighted MRI scans, linearly transformed to Talairach space) specially adapted for use with the MNI Linear Registration Package. . * average_305.mnc - a version of the average MRI that covers the whole brain (unlike the original Talairach atlas), sampled with 1mm cubic voxels * average_305_mask.mnc - a mask of the brain in average_305.mnc * average_305_headmask.mnc - another mask, required for nonlinear mode . Remark: Michael Hanke agreed to take over his stuff from mentors http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-autoreg and http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-autoreg-model to Debian Med svn and start group maintenance. Depends: mni-n3 Homepage: http://www.bic.mni.mcgill.ca/software/N3/ License: BSDish Responsible: Michael Hanke Pkg-URL: http://mentors.debian.net/debian/pool/main/m/mni-n3/ Pkg-Description: MNI Non-parametric Non-uniformity Normalization MNI Non-parametric Non-uniformity Normalization (N3). This package provides the 'nu_correct' tool for unsupervised correction of radio frequency (RF) field inhomogenities in MR volumes. Two packages are provided: * mni-n3 - provides 'nu_correct' * libebtks-dev - MNI support library with numerical types and algorithms . Remark: Michael Hanke agreed to take over his stuff from mentors http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-n3 to Debian Med svn and start group maintenance. Depends: brainvisa Homepage: http://brainvisa.info/ License: Free? (CeCill License) Pkg-Description: image processing factory for MR images BrainVISA is a software, which embodies an image processing factory. A simple control panel allows the user to trigger some sequences of treatments on series of images. These treatments are performed by calls to command lines provided by different laboratories. These command lines, hence, are the building blocks on which are built the assembly lines of the factory. BrainVISA is distributed with a toolbox of building blocks dedicated to the segmentation of T1-weighted MR images. The product of the main assembly line made up from this toolbox is the following: grey/white classification for Voxel Based Morphometry, Meshes of each hemisphere surface for visualization purpose, Spherical meshes of each hemisphere white matter surface, a graph of the cortical folds, a labeling of the cortical folds according to a nomenclature of the main sulci. Depends: lipsia Published-Title: Lipsia—a new software system for the evaluation of functional magnetic resonance images of the human brain Published-Authors: Gabriele Lohmann, Karsten Müller, Volker Bosch, Heiko Mentzel, Sven Hessler, Lin Chen, S. Zysset, D. Yves von Cramon Published-In: Computerized Medical Imaging and Graphics, 25: 449-457 Published-Year: 2001 Published-URL: http://www.medicalimagingandgraphics.com/article/S0895-6111(01)00008-8 Published-DOI: 10.1016/S0895-6111(01)00008-8 ; Added by blends-inject 0.0.5. [now official package] Depends: openmeeg-tools Published-Authors: Alexandre Gramfort, Théodore Papadopoulo, Emmanuel Olivi, Maureen Clerc Published-In: BioMedical Engineering OnLine 45:9 Published-Title: OpenMEEG: opensource software for quasistatic bioelectromagnetics Published-URL: http://www.biomedical-engineering-online.com/content/9/1/45 Published-Year: 2010 Depends: mricron Published-Title: Improving lesion-symptom mapping Published-Authors: Chris Rorden, Hans-Otto Karnath, Leonardo Bonilha Published-In: Journal of Cognitive Neuroscience, 19: 1081-1088 Published-Year: 2007 Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/17583985 Depends: itksnap Published-Title: User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability Published-Authors: Paul A. Yushkevich, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee, and Guido Gerig Published-In: Neuroimage, 31: 1116-1128 Published-Year: 2006 Published-DOI: 10.1016/j.neuroimage.2006.01.015 Depends: python-pypsignifit Homepage: http://psignifit.sourceforge.net/ License: MIT Language: C++, Python Responsible: Michael Hanke WNPP: 580499 Pkg-Description: fitting and testing hypotheses about psychometric functions This package allows fitting of psychometric functions to datasets while maintaining full control over a large number of parameters. Psignifit performs the calculation of confidence intervals as well as goodness-of-fit tests. . This is the successor of 'psignifit' a commandline-based toolbox. The new version is primarily a python module, but other bindings will be added eventually. Depends: python-statsmodels Depends: spm8 Registration: http://www.fil.ion.ucl.ac.uk/spm/software/download.html Homepage: http://www.fil.ion.ucl.ac.uk/spm/software/spm8/ License: GPL-2+ Responsible: NeuroDebian team WNPP: 592390 Pkg-Description: analysis of brain imaging data sequences Statistical Parametric Mapping (SPM) refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in software that is called SPM. It is designed for the analysis of fMRI, PET, SPECT, EEG and MEG. Published-Authors: Karl J. Friston, John T. Ashburner, Stephen Kiebel, Thomas E. Nichols and William D. Penny Published-Title: Statistical Parametric Mapping: The Analysis of Functional Brain Images. Published-In: Elsevier/Academic Press: Amsterdam Published-Year: 2007 Published-URL: http://www.elsevierdirect.com/product.jsp?isbn=9780123725608 Remark: This software is written for matlab, but initial tests indicate that some (significant) portion of it might also work with octave. More tests are pending... Depends: iqr Homepage: http://iqr.sourceforge.net License: GPL-3+ Responsible: NeuroDebian team Pkg-Description: large-scale multi-level neuronal systems simulator This graphical environment allows for designing large-scale multi-level neuronal systems that can control real-world devices, such as cameras and mobile robots, in real-time. iqr is an extensible framework with the ability to handle new, user-provided, neuron and synapse types, as well as custom interfaces to other hardware systems. iqr employes an XML-based format for system descriptions. Published-Authors: Ulysses Bernardet, Paul F.M.J. Verschure Published-Title: iqr: A tool for the construction of multi-level simulations of brain and behaviour. Published-In: Neuroinformatics, 8: 113-134 Published-Year: 2010 Published-DOI: 10.1007/s12021-010-9069-7 Depends: mriconvert ; Added by blends-inject 0.0.5. [Please note here if modified manually] Suggests: fieldtrip Homepage: http://fieldtrip.fcdonders.nl Language: Matlab/Octave WNPP: 605492 License: GPL-2+ Pkg-Description: toolbox for MEG and EEG analysis The software includes algorithms for simple and advanced analysis of MEG and EEG data, such as time-frequency analysis, source reconstruction using dipoles, distributed sources and beamformers and non-parametric statistical testing. It supports the data formats of all major MEG systems (CTF, Neuromag, BTi) and of the most popular EEG systems, and new formats can be added easily. FieldTrip contains high-level functions that you can use to construct your own analysis protocols in Matlab. Furthermore, it easily allows developers to incorporate low-level algorithms for new EEG/MEG analysis methods. Remark: The NIMH distributes a "port" of fieldtrip to Octave (at http://kurage.nimh.nih.gov/meglab/Meg/Software). It needs to be figured out whether this port can be incorporated into the official version, and to what degree it is complete. Packaging fieldtrip is required to complete the packaging of SPM8. ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: eeglab Homepage: http://sccn.ucsd.edu/eeglab Language: C, Matlab/Octave WNPP: 605739 Responsible: NeuroDebian Team License: GPL-2+ Pkg-URL: http://neuro.debian.net Pkg-Description: toolbox for processing and visualization of electrophysiological data EEGLAB is an interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data. Published-Authors: Delorme A and Makeig S Published-In: Journal of Neuroscience Methods 134:9-21 Published-Title: EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics Published-Year: 2004 Registration: http://sccn.ucsd.edu/eeglab/install.html ; Added by blends-inject 0.0.7. [s/pyxnat/python-pyxnat/] Depends: python-pyxnat ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: debruijn Homepage: http://www.cfn.upenn.edu/aguirre/wiki/public:de_bruijn_software Language: C++ Responsible: NeuroDebian Team License: BSD (4-clause) Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/debruijn.git Vcs-Git: git://git.debian.org/git/pkg-exppsy/debruijn.git Pkg-URL: http://neuro.debian.net/pkgs/debruijn.html Pkg-Description: De Bruijn cycle generator Continuous carry-over, fMRI experiments present stimuli in a counter-balanced sequence, meaning every stimulus precedes and follows every other. Higher level counterbalancing is useful to guard against some modeling assumptions of the approach and to test for the effects of stimulus history and context. Sequences that efficiently provide this control of stimulus order are called de Bruijn cycles. . This package provides a commandline tool to generate de Bruijn cycles. Published-Authors: GK Aguirre, MG Mattar, L Magis-Weinberg Published-DOI: 10.1016/j.neuroimage.2011.02.005 Published-In: NeuroImage 56: 1293-1300 Published-Title: de Bruijn cycles for neural decoding Published-Year: 2011 ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: freesurfer Homepage: http://surfer.nmr.mgh.harvard.edu/ Language: C/C++/Python/Perl/... Responsible: NeuroDebian Team License: BSD-style FreeSurfer Software License Agreement v1.0 Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/freesurfer.git Vcs-Git: git://git.debian.org/git/pkg-exppsy/freesurfer.git Pkg-URL: http://neuro.debian.net/pkgs/freesurfer.html Pkg-Description: analysis and visualization of functional brain imaging data FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. It contains a fully automatic structural stream for processing cross sectional and longitudinal data. . FreeSurfer provides many anatomical analysis tools, including: representation of the cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from the rest of the brain, skull stripping, B1 bias field correction, nonlinear registration of the cortical surface of an individual with an sterotaxic atlas, labeling of regions of the cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures, etc. Published-In: see http://surfer.nmr.mgh.harvard.edu/fswiki/Articles Registration: http://surfer.nmr.mgh.harvard.edu/fswiki/Registration Remark: The 'tktools' (tkmedit, tksurfer and tkregister2) under the CorTechs license are not readily redistributable thus excluded. ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: xnat Homepage: http://www.xnat.org Language: java WNPP: 629143 License: XNAT SLA Pkg-Description: platform for data management and productivity tasks in neuroimaging The primary functionality of XNAT is to provide a place to store and control access to neuroimaging data. This includes sophisticated user control, search and retrieval, and archiving capabilities. As open-source software, XNAT also supports a wide variety of research-based processing pipelines, and is able to link up with supercomputer processing power to dramatically shorten image processing time. Published-Authors: Marcus, D.S., Olsen T., Ramaratnam M., and Buckner, R.L. Published-In: Neuroinformatics 5(1): 11-34 Published-Title: The Extensible Neuroimaging Archive Toolkit (XNAT): An informatics platform for managing, exploring, and sharing neuroimaging data. Published-Year: 2007 Registration: http://www.xnat.org/download-xnat.html ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: pysurfer Homepage: http://pysurfer.github.com/ Language: Python WNPP: 641345 Responsible: NeuroDebian Team License: BSD-3 Pkg-Description: visualize Freesurfer's data in Python This is a Python package for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi’s powerful visualization engine with a high-level interface for working with MRI and MEG data. . PySurfer offers both a command-line interface designed to broadly replicate Freesurfer’s Tksurfer program as well as a Python library for writing scripts to efficiently explore complex datasets. ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: connectomeviewer Published-Authors: Gerhard S, Daducci A, Lemkaddem A, Meuli R, Thiran J-P and Hagmann P Published-DOI: 10.3389/fninf.2011.00003 Published-In: Front. Neuroinform. 5:3 Published-Title: The Connectome Viewer Toolkit: An open source framework to manage, analyze, and visualize connectomes Published-Year: 2011 ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: hid Homepage: http://www.nitrc.org/projects/hid Language: java License: BSD, BIRN Pkg-Description: database management system for clinical imaging The Human Imaging Database (HID) is an extensible database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large. Published-Authors: Keator, D.B.; Grethe, J.S.; Marcus, D.; Ozyurt, B.; Gadde, S.; Murphy, S.; Pieper, S.; Greve, D.;Notestine, R.; Bockholt, H.J.; Papadopoulos, P. Published-In: IEEE Transactions on Information Technology in Biomedicine, 12 (2) Published-Title: A National Human Neuroimaging Collaboratory Enabled By The Biomedical Informatics Research Network (BIRN) Published-Year: 2008 Registration: http://www.nitrc.org/account/register.php debian-science-1.0ubuntu1/tasks/physics-dev0000644000000000000000000000045712131260661015727 0ustar Task: Physics-dev Description: Debian Science Physics-dev packages This metapackage will install Debian Science packages which might be helpful for development of applications for Mathematics. . You might also be interested in the science-physics metapackage. Depends: freefoam-dev Depends: pyfai debian-science-1.0ubuntu1/tasks/psychophysics0000644000000000000000000002226011673216755016414 0ustar Task: Psychophysics Description: Debian Science packages for Psychophysics This metapackage will install Debian packages which might be useful for carrying out any experiment relating physical stimuli and their psychological effects. . The selection of packages is targeting software for stimuli delivery. For additional software related to the analysis of the acquired data refer to science-neuroscience-cognitive, med-imaging depending on the domain of application. Additionally look into science-bci since those often provide a complete loop frameworks including stimuli delivery. Suggests: science-neuroscience-cognitive Meta-Suggests: svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/neuroscience-cognitive Suggests: science-bci Meta-Suggests: svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/bci ; Added by blends-inject 0.0.6. [Please note here if modified manually] Depends: psychopy Pkg-URL: http://neuro.debian.net/pkgs/psychopy.html Published-Authors: J. W. Peirce Published-DOI: 10.1016/j.jneumeth.2006.11.017 Published-In: Journal of Neuroscience Methods, 162:8-13 Published-Title: PsychoPy - Psychophysics software in Python Published-Year: 2007 ; Added by blends-inject 0.0.6. [Please note here if modified manually] Suggests: visionegg Homepage: http://www.visionegg.org WNPP: 365856 License: LGPL Pkg-Description: Python library for 2D/3D visual stimulus generation The Vision Egg is a programming library that uses standard, inexpensive computer graphics cards to produce visual stimuli for vision research experiments. Published-Authors: Andrew Straw Published-DOI: 10.3389/neuro.11.004.2008 Published-In: Frontiers in Neuroinformatics Published-Title: Vision Egg: An Open-Source Library for Realtime Visual Stimulus Generation Published-URL: http://frontiersin.org/neuroinformatics/paper/10.3389/neuro.11/004.2008/ Published-Year: 2008 Depends: python-pyoptical Depends: python-pyepl ; Added by blends-inject 0.0.7. [Please note here if modified manually] Recommends: octave-psychtoolbox-3 Homepage: http://psychtoolbox.org Language: Matlab/Octave, C WNPP: 606557 Responsible: NeuroDebian Team License: GPL-2+ Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/psychtoolbox-3.git Vcs-Git: git://git.debian.org/git/pkg-exppsy/psychtoolbox-3.git Pkg-URL: http://neuro.debian.net/pkgs/octave-psychtoolbox-3.html Pkg-Description: toolbox for vision research -- Octave bindings Psychophysics Toolbox Version 3 (PTB-3) is a free set of Matlab and GNU/Octave functions for vision research. It makes it easy to synthesize and show accurately controlled visual and auditory stimuli and interact with the observer. . The Psychophysics Toolbox interfaces between Matlab or Octave and the computer hardware. The Psychtoolbox's core routines provide access to the display frame buffer and color lookup table, allow synchronization with the vertical retrace, support millisecond timing, allow access to OpenGL commands, and facilitate the collection of observer responses. Ancillary routines support common needs like color space transformations and the QUEST threshold seeking algorithm. . This package contains bindings for Octave. ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: python-pyxid ; Added by blends-inject 0.0.6. [now official package] Depends: libfreenect-dev ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: tscope Homepage: http://users.ugent.be/~masteven/tscope Language: C License: GPL Pkg-Description: C/C++ experiment programming library for cognitive scientists Tscope is a C/C++ experiment programming library for cognitive scientists. It provides functions for graphics, sound, timing, randomization and response registration. Published-Authors: Stevens, M., Lammertyn, J., Verbruggen, F., & Vandierendonk, A. Published-In: Behavior Research Methods, 38, 280-286. Published-Title: Tscope: A C library for programming cognitive experiments on the MS Windows platform Published-Year: 2006 Remark: Primarily targeting Windows platform, provides some functionality on Linux ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: opensesame Homepage: http://www.cogsci.nl/software/opensesame WNPP: 611640 Responsible: Sebastiaan Mathôt License: GPL-3 Pkg-URL: http://files.cogsci.nl/software/opensesame/ Pkg-Description: graphical experiment builder for the social sciences OpenSesame is a graphical experiment builder. OpenSesame provides an easy to use, point-and-click interface for creating psychological experiments. In addition to a powerful sketchpad for creating visual stimuli, OpenSesame features a sampler and synthesizer for sound playback. For more complex tasks, OpenSesame supports Python scripting using the built-in editor with syntax highlighting. Published-Authors: Mathôt, S., & Theeuwes, J. Published-In: http://www.cogsci.nl/software/opensesame Published-Title: OpenSesame (Version 0.22) [Computer software and manual] Published-Year: Retrieved December 18, 2010 ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: psytoolkit Homepage: http://psytoolkit.leeds.ac.uk Language: Ruby License: GPL-3+ Pkg-URL: http://psytoolkit.leeds.ac.uk/download-installation.html Pkg-Description: programming and running psychological experiments Psytoolkit offers * Scripting language designed for psychological experiments: o Structure designed for experiments (tasks/trials/trial lists/random selection/blocks). o Use of bitmaps (png,jpeg,tiff,and many more). o Use of MPEG videos. o Read from keyboard, mouse, and external devices. o Voicekey support via IoLab device o Easy programming of parallel port and advanced IO cards. o Use of variables. o Conditional expressions (if/then/while). o Easy interfacing with statistical software R for online feedback to participants. o Easy interfacing with C language. o It is easy to use. * Easy functions for visual and auditory stimulus presentation. * Precise timing of stimulus presentation and data collection. * Can be used as scripting language, but also comes with a C-library. * Comes with a questionnaire presenter psyquest * Online Documentation. Remark: Depends on libhid removed from Debian due to needed TLC ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: debruijn Homepage: http://www.cfn.upenn.edu/aguirre/wiki/public:de_bruijn_software Language: C++ Responsible: NeuroDebian Team License: BSD (4-clause) Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/debruijn.git Vcs-Git: git://git.debian.org/git/pkg-exppsy/debruijn.git Pkg-URL: http://neuro.debian.net/pkgs/debruijn.html Pkg-Description: De Bruijn cycle generator Continuous carry-over, fMRI experiments present stimuli in a counter-balanced sequence, meaning every stimulus precedes and follows every other. Higher level counterbalancing is useful to guard against some modeling assumptions of the approach and to test for the effects of stimulus history and context. Sequences that efficiently provide this control of stimulus order are called de Bruijn cycles. . This package provides a commandline tool to generate de Bruijn cycles. Published-Authors: GK Aguirre, MG Mattar, L Magis-Weinberg Published-DOI: 10.1016/j.neuroimage.2011.02.005 Published-In: NeuroImage 56: 1293-1300 Published-Title: de Bruijn cycles for neural decoding Published-Year: 2011 Depends: nrec Homepage: http://nrec.neurologie.uni-tuebingen.de/nrec License: GPL Language: C++ Pkg-Description: neurological stimulation, data acquisition and experiment control Nrec , developed by Friedemann Bunjes and Jan Gukelberger at the Neurology of Tübingen University, is a package for stimulation, data acquisition and experiment control in the flavour of cognitive fMRI research, which has been expanded to include flexible biosignal acquisition and sensory stimulation. It produces Matlab-readable files and generally puts an emphasis on standards like using the comedi Linux data acquisition library, OpenGL, XML parameter file format and hdf5 data storage files format. ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: psychlops Homepage: http://psychlops.sourceforge.jp Language: C++ License: GPL Pkg-Description: Psychlops is a free C++ library to offer the easy way to develop a demonstration of various types of visual stimulus used in the Vision science. . Binary builds are available only for OS X and Windows. Sources available from sf's SVN: http://sourceforge.jp/projects/psychlops/svn/view/cpp/ ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: pebl Homepage: http://pebl.sourceforge.net Language: C++ WNPP: 650775 License: GPL Pkg-Description: platform for psychology experiments PEBL (Psychology Experiment Building Language) is a system designed for creating psychology and neuroscience experiments and tests. It offers a simple programming language tailor-made for creating and conducting many standard experiments. Published-Authors: Mueller, S. T. Published-ISBN: 978-0-557-65817-6 Published-In: Lulu press Published-Title: The PEBL Manual Published-Year: 2011 debian-science-1.0ubuntu1/tasks/mathematics-dev0000644000000000000000000000410512264701150016536 0ustar Task: Mathematics-dev Description: Debian Science Mathematics-dev packages This metapackage will install Debian Science packages which might be helpful for development of applications for Mathematics. . You might also be interested in the science-mathematics metapackage. Depends: libmesh-dev Why: FEA Depends: libnglib-dev Why: FEA, mesh generator Suggests: libtet1.4.2-dev Why: non-free Depends: python-numpy Depends: libgsl0-dev Depends: liblapack-dev, libatlas-base-dev, libblas-dev Depends: libsuperlu3-dev Why: solver Depends: libglpk-dev Why: linear programming Depends: libcgal-dev Why: computational geometry Depends: libmatheval-dev Depends: python-openopt Depends: libmatio-dev Depends: libblitz0-dev Depends: libjama-dev, libtnt-dev, liblip-dev, libranlip-dev Why: Requested by Aníbal Monsalve Salazar Depends: libarpack2-dev Depends: libmei-dev Depends: libarmadillo-dev Suggests: libitpp-dev Suggests: libnauty-dev Suggests: liblrs-dev Depends: libstxxl-dev Depends: libnewmat10-dev Depends: libmadlib-dev Why: Mesh adaptation Depends: libslepc3.0.0-dev Why: Generalized and standard eigenvalue solver framework Depends: petsc-dev, libtrilinos-dev Suggests: libqrupdate-dev Depends: liblife-dev Why: Partial differential equations library, FEA, CFD Suggests: python-openturns, libopenturns-dev, openturns-examples Why: Uncertainty quantification in numerical simulation Depends: libqd-dev Why: double-double and quad-double precision C++ datatypes Depends: libcqrlib2-dev Suggests: cfortran Depends: libcvector2-dev Depends: libhypre-dev Depends: libitsol-dev Depends: libmuparser-dev Depends: libcneartree-dev Depends: libsparskit-dev Depends: libspooles-dev Depends: libsuitesparse-dev Depends: ufc, python-ufc, python-ffc Depends: python-ufl Depends: libscythestat-dev Depends: libfreefem++-dev, libfreefem-dev Depends: libgivaro-dev Suggests: givaro-dev-doc, givaro-users-doc Depends: fflas-ffpack Suggests: fflas-ffpack-dev-doc, fflas-ffpack-user-doc Depends: liblevmar-dev Depends: libpolybori-dev, libpolybori-groebner-dev, python-polybori debian-science-1.0ubuntu1/tasks/imageanalysis0000644000000000000000000000505312264700327016321 0ustar Task: Image analysis Description: Debian Science image analysis packages This metapackage will install Debian Science packages related to scientific image acquisition. This might be used in several sciences (as for instance science-dataacquisition, science-viewing and science-typesetting). Depends: gpivtools, gpiv Why: Particle image velocitometry Depends: libcv-dev Why: Computer vision library Depends: gwyddion Why: Scanning Probe Microscopy (SPM) data visualization and analysis Suggests: scilab-sivp Depends: libteem2 Suggests: cimg-dev Suggests: libsimage-dev Suggests: libvisad-java WNPP: 641399 Responsible: Mathieu Malaterre Homepage: http://www.ssec.wisc.edu/~billh/visad.html License: GPL, LGPL, BSD Language: Java Pkg-Description: Visualization for Algorithm Development VisAD is a Java component library for interactive and collaborative visualization and analysis of numerical data. The name VisAD is an acronym for "Visualization for Algorithm Development". The system combines: . The use of pure Java for platform independence and to support data sharing and real-time collaboration among geographically distributed users. Support for distributed computing is integrated at the lowest levels of the system using Java RMI distributed objects. . A general mathematical data model that can be adapted to virtually any numerical data, that supports data sharing among different users, different data sources and different scientific disciplines, and that provides transparent access to data independent of storage format and location (i.e., memory, disk or remote). The data model has been adapted to netCDF, HDF-5, FITS, HDF-EOS, McIDAS, Vis5D, GIF, JPEG, TIFF, QuickTime, ASCII and many other file formats. . A general display model that supports interactive 3-D, data fusion, multiple data views, direct manipulation, collaboration, and virtual reality. The display model has been adapted to Java3D and Java2D and used in an ImmersaDesk virtual reality display. . Data analysis and computation integrated with visualization to support computational steering and other complex interaction modes. . Support for two distinct communities: developers who create domain- specific systems based on VisAD, and users of those domain-specific systems. VisAD is designed to support a wide variety of user interfaces, ranging from simple data browser applets to complex applications that allow groups of scientists to collaboratively develop data analysis algorithms. . Developer extensibility in as many ways as possible. debian-science-1.0ubuntu1/tasks/physics0000644000000000000000000001615212125512567015162 0ustar Task: Physics Description: Debian Science Physics packages This metapackage will install Debian Science packages related to Physics. You might also be interested in the debtag field::physics and, depending on your focus, in education-physics metapackage. Depends: cernlib, geant321, paw++, paw Suggests: paw-demos Depends: clhep WNPP: 636972 Responsible: Lifeng Sun Homepage: http://proj-clhep.web.cern.ch/proj-clhep/ License: GPL-3, LGPL-3 Language: C++ Pkg-Description: Class Library for High Energy Physics The CLHEP package is a set of High Energy Physics specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. Depends: geant4 Homepage: http://geant4.cern.ch/ License: GPL Pkg-URL: http://lcg-heppkg.web.cern.ch/lcg-heppkg/debian Pkg-Description: toolkit for the simulation of the passage of particles through matter Geant4 is a toolkit for the simulation of the passage of particles through matter. Its application areas include high energy physics and nuclear experiments, medical, accelerator and space physics studies. The Geant4 software consists of an extensive set of libraries, fundamentally object-oriented and based in modern C++. Depends: abinit | mpqc | openmx | psi3 Why: Abinitio Quantum mechanics (As psi3 doesn't do DFT, maybe it should be excluded) Depends: gerris Depends: feynmf Depends: freefoam Depends: fityk Depends: horae, ifeffit, sixpack Depends: tessa | tessa-mpi Depends: science-numericalcomputation Why: numerical programming environments similar to Matlab/IDL Depends: opencascade-draw Depends: science-electronics Depends: v-sim Depends: gpiv, gpivtools Depends: maxima Why: Symbolic maths Depends: python-sympy Why: Symbolic maths Depends: axiom Why: Symbolic maths Suggests: science-statistics, science-mathematics Suggests: scilab-sivp Depends: meshlab Depends: cadabra Depends: drawxtl Depends: opticalraytracer Depends: ghkl Depends: python-deap Suggests: life-apps, liblife-dev Why: Partial differential equation library, FEA, CFD Depends: etsf-io Depends: pymca Depends: quantum-espresso Depends: gwyddion Depends: blzpack Homepage: http://crd.lbl.gov/~osni/#Software WNPP: 435394 License: BSD Responsible: Ondrej Certik Pkg-Description: library for solving large sparse eigenproblems BLZPACK (for Block LancZos PACKage, release 04/00) is a standard Fortran 77 implementation of the block Lanczos algorithm intended for the solution of the standard eigenvalue problem Ax=µx or the generalized eigenvalue problem Ax=µBx, where A and B are real, sparse symmetric matrices, µ an eigenvalue and x an eigenvector. . The development of this eigensolver was motivated by the need to solve large, sparse, generalized problems from free vibration analyses in structural engineering. Several upgrades were performed afterwards aiming at the solution of eigenvalues problems from a wider range of applications. . Documentation: user's guide, technical report and comprehensive bibliography. . Install this package if you need to compile or link against BLZPACK. Depends: gate Homepage: http://opengatecollaboration.healthgrid.org/ WNPP: 431425 License: LGPL Responsible: Nicolas Spalinger Pkg-Description: Geant4 Application for Emission Tomography GATE incorporates the Geant4 libraries in a modular, versatile, and scripted simulation toolkit which is adapted to the field of nuclear medicine both in PET (Positron Emission Tomography) and SPECT (Single Photon Emission Computer Tomography). It allows the accurate description of time-dependent phenomena such as source or detector movement and source decay kinetics. The ability to synchronize all time-dependent components allows a coherent description of the acquisition process. It makes it possible to perform realistic simulations of data acquisitions in time. Depends: openfoam License: GPL Homepage: http://www.opencfd.co.uk/openfoam/ Pkg-Description: Computational fluid dynamics application The OpenFOAM (Open Field Operation and Manipulation) CFD Toolbox can simulate anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics, electromagnetics and the pricing of financial options. Remark: will probably never enter Debian According to https://lists.debian.org/debian-science/2012/06/msg00049.html packaging would be really complex and it contains some non-free components. Freefoam (see above) is some kind of plugin replacement. Depends: jfreemesh Homepage: http://dev.artenum.com/projects/JFreeMesh License: QPL Pkg-Description: 3D mesh library in Java JFreeMesh is a 3D mesh library written in Java and providing a high level API for mesh manipulation. JFreeMesh is based on a descending mesh data structure but simulate a full connectivity mesh by providing optimized method to access to any upper mesh element by using the global mesh methods. Therefore, JFreeMesh allows to load a large amount of mesh elements for a small memory foot print. JFreeMesh comes with a default mesh loader based on the GMSH file format and provides, through the JFreeMesh-VTK package, an exporter to VTK. . Depends: spis Homepage: http://dev.spis.org/projects/spine/home/spis License: GPL Pkg-Description: Software toolkit for spacecraft-plasma interactions modelling JSPIS stands for Spacecraft Plasma Interaction System. SPIS project aims at developing a software toolkit for spacecraft-plasma interactions modelling. Depends: espresso++ Homepage: http://espresso.scai.fraunhofer.de/ License: Not yet known (hopefully free) Pkg-Description: Extensible Simulation Package for Research on Soft matter ESPResSo is a highly versatile software package for the scientific simulation and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research, with emphasis on charged systems. Depends: cp2k X-Removed: Packages removed from Debian Depends: octaviz Pkg-URL: http://snapshot.debian.org/package/octaviz/ Homepage: http://octaviz.sourceforge.net/ Pkg-Description: 3D visualization system for Octave Octaviz is a visualization system for Octave. It is a wrapper that makes all VTK classes accessible from within Octave using the same object-oriented syntax as in C++ or Python. Octaviz also provides high-level functions for 2D and 3D visualization. Using those functions, most common visualization tasks (3D surface plots, contour plots etc) can be accomplished without any knowledge about VTK. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/535537 Depends: root-system Depends: libroot-tmva-dev, libroot-montecarlo-vmc-dev, libroot-math-mlp-dev X-Comment: Somebody injected the libraries from the ROOT system explicitely here for physics - so these are included since root-system is packaged again X-Suggests: root-plugin-fftw3, libroot-mathmore5.18 In case these packages will be created in root-system these need to be added here as well. Depends: fdmnes Pkg-URL: http://people.debian.org/~tille/packages/fdmnes/ debian-science-1.0ubuntu1/tasks/bci0000644000000000000000000001535412132746777014252 0ustar Task: Brain-computer interface Metapackage: false Description: Debian Science packages for the design and use of brain-computer interface (BCI) -- direct communication pathway between a brain and an external device. BCIs are often aimed at assisting, augmenting or repairing human cognitive or sensory-motor functions. . The selection of packages is targeting the complete frameworks for the design of BCI systems. Often such systems rely on external presentation, data collection and analysis software which could be found in science-neuroscience-cognitive, science-dataacquisition, data-machine-learning metapackages. ; Added by blends-inject 0.0.6. [Please note here if modified manually] Suggests: pyff Homepage: http://bbci.de/pyff/ Language: Python License: GPL-2+ Vcs-Browser: https://github.com/venthur/pyff Vcs-Git: git://github.com/venthur/pyff.git Pkg-Description: Brain Computer Interface (BCI) framework Pyff is a Pythonic Feedback Framework which provides a platform independent framework to develop BCI feedback applications in Python. It was designed to make the development of feedback applications as easy as possible. Pyff framework moves feedback implementations to a general purpose, and easy to learn language like Python. Python provides many so called bindings to other libraries, which allow it to develop high quality multimedia feedback applications, with little effort. . The framework communicates with the rest of the BCI system via a standardized communication protocol using UDP and XML and is therefore suitable to be used with any BCI system that may be adapted to send its control signal via UDP in the specified format. Published-Authors: Bastian Venthur, Simon Scholler, John Williamson, Sven Dähne, Matthias S Treder, Maria T Kramarek, Klaus-Robert Müller and Benjamin Blankertz Published-DOI: 10.3389/fnins.2010.00179 Published-In: Frontiers in Neuroscience Published-Title: Pyff --- A Pythonic Framework for Feedback Applications and Stimulus Presentation in Neuroscience Published-Year: 2010 ; Added by blends-inject 0.0.6. [Please note here if modified manually] Suggests: pybci Homepage: http://pybci.sourceforge.net/ Language: Python, C++ License: MIT Vcs-Browser: http://pybci.git.sourceforge.net/git/gitweb-index.cgi Vcs-Git: git://pybci.git.sourceforge.net/gitroot/pybci/pybci Pkg-Description: Brain Computer Interface module for Brain Vision Recorder This module gives you the possibility to create a Brain Computer Interface (BCI), and herewith to get EEG data online and evaluate the data while you are receiving it. The module is made for all users of the Brain Vision Recorder because of the therein implemented function of Remote Data Access. It is not possible to use it with another EEG Recorder Software, but this will be a project in the future. . Using the PyBCI module, you are able to get a numpy data array in up to every few ten milliseconds and therewith evaluate the data almost in realtime with other powerful Python packages, for example using PyMVPA. Remark: No activity since Sep 2009 ; Added by blends-inject 0.0.6. [Please note here if modified manually] Suggests: bcpy2000 Homepage: http://bci2000.org/downloads/BCPy2000/BCPy2000.html Language: Python, C++ License: LGPL-3+ and GPL-3+ and non-free (BCI2000) Pkg-Description: platform for brain-computer interface systems BCPy2000 provides a platform for rapid, flexible development of experimental brain-computer interface systems. It is based on, and hosted by, the BCI2000 project. From the developer's point of view, the implementation is carried out in Python, taking advantage of various high-level packages: VisionEgg for stimulus presentation, NumPy and SciPy for signal processing and classification, and IPython for interactive debugging. . Being a BCI2000 system, it is modular, consisting of an Application module (the stimulus presentation part), a Signal Processing module (the machine-learning part), and a Signal Source module (the toy data generation part). You can choose to use Python to implement one, two, or all three of these modules, and use other pre-existing BCI2000 modules for the remainder of the system (for example, for the Signal Source, you can choose from BCI2000's comprehensive range of EEG acquisition modules). The modules communicate over TCP/IP, so they can run on different machines (and possibly different operating systems) if necessary. ; Added by blends-inject 0.0.6. [Please note here if modified manually] Suggests: bci2000 Homepage: http://bci2000.org Language: C++ License: non-free (non-redistributable, non-commercial) Pkg-Description: platform for brain-computer interface systems BCI2000 supports a variety of data acquisition systems, brain signals, and study/feedback paradigms. During operation, BCI2000 stores data in a common format (BCI2000 native or GDF), along with all relevant event markers and information about system configuration. BCI2000 also includes several tools for data import/conversion (e.g., a routine to load BCI2000 data files directly into Matlab) and export facilities into ASCII. . BCI2000 also facilitates interactions with other software. For example, Matlab scripts can be executed in real-time from within BCI2000, or BCI2000 filters can be compiled to execute as stand-alone programs. Furthermore, a simple network-based interface allows for interactions with external programs written in any programming language. For example, a robotic arm application that is external to BCI2000 may be controlled in real time based on brain signals processed by BCI2000, or BCI2000 may use and store along with brain signals behavioral-based inputs such as eye-tracker coordinates. Registration: http://www.bci2000.org/MTA Remark: Besides non-commercial restriction, it is required that "ACADEMIC USER must be an investigator / lab director (and not a post-doc or student)". Re-distribution (to third-party) is also forbidden. ; Added by blends-inject 0.0.6. [Please note here if modified manually] Suggests: emokit Homepage: https://github.com/daeken/Emokit Language: Python, C License: BSD-3 Vcs-Browser: https://github.com/daeken/Emokit Vcs-Git: git://github.com/daeken/Emokit.git Pkg-Description: Emotiv EPOC headset Python interface Emotive is an interface to a budget Emotiv EPOC EEG headset. ; Added by blends-inject 0.0.6. [Please note here if modified manually] Suggests: openvibe Homepage: http://openvibe.inria.fr Language: C++ WNPP: 580247 License: LGPL Pkg-Description: platform for the design, test and use of BCI OpenViBE enables to design, test and use Brain-Computer Interfaces (BCI). OpenViBE is a software for real-time neurosciences (that is, for real-time processing of brain signals). It can be used to acquire, filter, process, classify and visualize brain signals in real time. debian-science-1.0ubuntu1/tasks/numericalcomputation0000644000000000000000000000503411766077766017760 0ustar Task: Numerical Computation Description: Debian Science Numerical Computation packages This metapackage will install Debian Science packages useful for numerical computation. The packages provide an array oriented calculation and visualisation system for scientific computing and data analysis. These packages are similar to commercial systems such as Matlab and IDL. Depends: octave Why: numerical programming environment similar to Matlab Depends: python-matplotlib, python-scipy, ipython, python-numpy, spyder, python-guiqwt Why: Python based numerical programming environment similar to Matlab Depends: pdl Why: Perl based numerical programming environment similar to Matlab Depends: gnudatalanguage Why: numerical programming environment compatible with IDL Depends: scilab, scilab-sivp, scilab-scimax, scilab-swt, scilab-ann, scilab-plotlib Depends: freemat Depends: yorick Depends: r-base Why: S is the statistician's Matlab and R is to S what Octave is to Matlab. Depends: qtoctave Depends: lush Why: environment for prototyping large numeric computations in Lisp Depends: yade Why: platform for discrete element modeling Depends: liggghts Why: open source discrete element method particle simulation code Depends: esys-particle Why: Open Source software for particle-based numerical modelling. The software implements the Discrete Element Method (DEM). Suggests: hpcc Depends: python-scitools Depends: python-deap Depends: octavede Homepage: http://octavede.sourceforge.net/ Pkg-URL: http://snapshot.debian.org/package/octavede/0.3-1/ Pkg-Description: development environment for the Octave mathematical software OctaveDE is a development environment for the Octave mathematical software package. Octave normally is run in a terminal. Octavede provides an GTK/X11 application that provides functionality similar to other mathematical software packages. Remark: Removed from Debian This package was removed from Debian but some versions are available from http://snapshot.debian.org/ . Reasons are given here: http://bugs.debian.org/534362 . It seems that qtoctave might be considered as replacemenet. Depends: lammps Why: LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. debian-science-1.0ubuntu1/tasks/distributedcomputing0000644000000000000000000000561012264700327017742 0ustar Task: Distributed Computing Description: Debian Science Distributed Computing packages This metapackage will install Debian Science packages useful for various types of distributed computing, such as grid-, cloud-, cluster- and parallel-computing. Depends: ipython Why: Provides ipcluster/ipcontroller/ipengine for Python-based distributed computing Depends: torque-common, torque-server Depends: libarccommon2 Depends: gridengine-client, gridengine-exec, gridengine-master, gridengine-qmon Depends: globus-core Depends: openmpi-bin, mpich2 Depends: openmpipython, mpich2python, python-mpi Suggests: hpcc ; Added by blends-inject 0.0.7. [now official package] ; yoh: manually adjusted to Depends: Depends: condor Published-Authors: Michael Litzkow, Miron Livny, and Matt Mutka Published-In: Proceedings of the 8th International Conference of Distributed Computing Systems, pp. 104-111 Published-Title: Condor - A Hunter of Idle Workstations Published-Year: 1988 Registration: http://www.cs.wisc.edu/condor/downloads-v2/ Suggests: coop-computing-tools Published-Authors: Douglas Thain, Christopher Moretti, and Jeffrey Hemmes Published-DOI: 10.1007/s10723-008-9100-5 Published-In: Journal of Grid Computing, 7, 51-72 Published-Title: Chirp: A Practical Global Filesystem for Cluster and Grid Computing Published-Year: 2009 ; Added by blends-inject 0.0.7. [now official package] Suggests: python-mpi4py ; Added by blends-inject 0.0.7. [Please note here if modified manually] Depends: dmtcp Published-Authors: Jason Ansel, Kapil Arya, and Gene Cooperman Published-In: 23rd IEEE International Parallel and Distributed Processing Symposium (IPDPS'09). Published-Title: DMTCP: Transparent Checkpointing for Cluster Computations and the Desktop Published-Year: 2009 ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: psom Homepage: http://code.google.com/p/psom/ Language: Matlab/Octave Responsible: NeuroDebian Team License: MIT/Expat Pkg-Description: pipeline system for Octave and Matlab PSOM is a lightweight library to manage complex multi-stage data processing. A pipeline is a collection of jobs, i.e. Matlab or Octave code with a well identified set of options that are using files for inputs and outputs. To use PSOM, the only requirement is to generate a description of a pipeline in the form of a simple Matlab/Octave structure. PSOM then automatically offers the following services: . * Run jobs in parallel using multiple CPUs or within a distributed computing environment. * Generate log files and keep track of the pipeline execution. These logs are detailed enough to fully reproduce the analysis. * Handle job failures: successful completion of jobs is checked and failed jobs can be restarted. * Handle updates of the pipeline: change options or add jobs and let PSOM figure out what to reprocess. Depends: environment-modules debian-science-1.0ubuntu1/tasks/meteorology-dev0000644000000000000000000000554712264700327016624 0ustar Task: Meteorology-dev Description: Debian Science Meteorology-dev packages This metapackage will install Debian Science packages which might be helpful for development of applications for Meteorology and Climate. . You might also be interested in the science-meteorology metapackage. Depends: libemos-dev Why: standard library for BUFR formats Depends: libgadap-dev Depends: libcmor-dev Pkg-Description: Development files for Climate Model Output Rewriter The "Climate Model Output Rewriter" (CMOR, pronounced "Seymour") comprises a set of C-based functions, with bindings to both python and FORTRAN 90, that can be used to produce CF-compliant netCDF files that fulfill the requirements of many of the climate community's standard model experiments. These experiments are collectively referred to as MIP's and include, for example, AMIP, CMIP, CFMIP, PMIP, APE, and IPCC scenario runs. The output resulting from CMOR is "self-describing" and facilitates analysis of results across models. Depends: libgrib-api-dev, libgrib-api-tools Why: grib-api is the standard library for GRIB2 file management. Depends: libgrib2c-dev Why: API for reading GRIB2 files Depends: libhe5-hdfeos-dev Why: EOS extensions to the HDF library, for Earth Observation datatypes. Depends: libhe4-hdfeos-dev Why: EOS extensions to the HDF library, for Earth Observation datatypes. Pkg-Description: Extension to HDF4 to support Earth Observing System datatypes HDF-EOS is a software library that is an extension of National Center for Supercomputing Applications (NCSA) HDF. The library supports the construction of new data structures: Grid, Point and Swath. . This version is built against the HDF4 Depends: libproj-dev Why: Needed for many cartographic tasks (eg coastlines on maps) Depends: libgctp-dev Depends: libnetcdf-dev, netcdf-bin Depends: liblapack-dev, libblas-dev, libfftw3-dev Why: Most forecasting codes use BLAS and LAPACK Depends: libblas-doc, liblapack-doc, libfftw3-doc Depends: liblas-dev Depends: libspherepack-dev Depends: libterralib-dev Suggests: gfortran Why: Much meteorological code is developed in Fortran. Suggests: ksh Why: Many Meteorology codes use ksh as their scripting shells. Suggests: pkg-config Why: Simplifies the scripting of builds. Depends: liboasis3-dev Why: Coupler used by many climate models. Needed by some NWP models to compile. (or stubs for the same routines) Depends: libudunits2-dev Why: widely used in climate models. Depends: libdap-dev Why: used by GrADS, NCL , etc. to retrieve netcdf and other large data files. Depends: python-openturns, libopenturns-dev, openturns-examples Why: Uncertainty quantification in numerical simulation Suggests: liblife-dev Why: Partial differential equations library, FEA, CFD Depends: wcslib-dev, wcslib-doc Why: Co-ordinates system for geographical data in FITS files Depends: freefoam-dev Depends: librsl-dev